Since it seems the changelogs on the downloads page are not maintained, here are the changelogs from Steam's product page. Starting where Gog's Changelog page seems to stop.

(2023-08-27) Hot-Fix v1.3.3

• Fix: Ensure door lock state can't get out of sync with door open state

(2023-09-09 Patch Notes v1.3.4
• Change: Download tool now persists current selection between uses
• Fix: Grenade wasn't rotating in your 'hand'
• Fix: A light was poorly configured in the Prelude

(2023-09-24) Patch Notes v1.3.5
• Fix: MUM was occasionally thinking she was being obstructed by herself
• Change: "Can be used as a torch" added to Download upgrade description
• Improvement: Tweak lighting in the storage area above loading bay 1 at the Freight Workshop
• Improvement: Tweak lighting in the pup vents behind the Simplex at CRS Engineering
• No change: Checked in all kinds of ways that anti-aliasing is definitely definitely definitely working so I still don't know why people keep telling me it isn't

(2023-09-28) Patch Notes v1.3.6
• Fix: Drop/Throw controls were showing up as '?' when using game controller
• Fix: The text that tries to explain your PUP is safe was missing the word "safe". Caused by a change I made to the way feminine forms of adjectives load.

(2023-10-07) Patch Notes v1.3.7
• Fix: Rocketing around while carrying stuff - the thing being carried was being considered something you could rocket into, with potentially annoying consequences - with this update the thing being carried is now considered 'an extension of you' and will travel with you without obstructing your path.
• Improvement: VaQ self-suck physics was all over the place, wasn't this bad originally I swear. With this patch it's a lot less frustrating to suck yourself towards things using the VaQ.

(2023-10-29) Patch Notes v1.3.8
• Improvement: With the Shift tool equipped from the tool wheel, you can now collect worms and interact generally - it was inconsistent that you couldn't.
• Fix: Discovered and corrected case where some robots could spawn out of bounds when loading saves under certain situations

(2023-11-23) Patch Notes v1.3.9
• Fix: Some sensors weren't selectable with the 'ego mode as a toggle input action' key-binding setting enabled

(2023-11-25) Patch Notes v1.3.10
• Fix: Merging Station left-side stairs collision was slightly off
• Fix: Evil Eye on those stairs could see through external wall
• Fix: Prevent worm from being collected through ceiling

(2023-12-20) Patch Notes v1.3.11
• Fix: One particular bad-bug-bot was loading in too late in Conscious Robot Services Lobby area
• Fix: Merging Station train - hopeful fix for a case where the train appeared very much derailed, but its internal state considered not derailed.

(2024-01-06) Patch Notes v1.3.12
• Fix: Merging Station train - after another train derailment report, now done something to make bad derailments auto-re-rail.
• Fix: If Parasite goes AWOL, bring it back
• Fix: Camera nearclip artefacts were showing under some circumstances when very wide FOV setting used

(2024-01-30) Patch Notes v1.3.13
• NEW: While in ctrl of a Performance Monitor (Perf Mon - the big display screen that among other things tells you how many resources remain in the current area) - you can now hold the 'thrust' button (Spacebar on PC) to execute a scan to reveal the location of all remaining EGO points in the area.
Quite a number of you have been asking for something along these lines. I'm resisting adding something that completely gives away EGO locations because there are one or two interesting cases that would be spoiled - so you still have to 'work' a bit to find them, but at least now you can get a clue about roughly where to go looking.

• Fix: Added missing colliders to a specific section in the Launch Ctrl level
• Fix: Added fatter colliders around some pipes in Launch Ctrl level to reduce chance of physics glitching through them
• Fix: Prevent HOP to PUP in bug-box before bug-box has been opened.
• Fix: A few typos corrected in the English version

(2024-02-18) Patch Notes v1.3.14
• NEW: German localization of the game is now available.
• NEU: Eine deutsche Übersetzung des Spiels ist jetzt verfügbar.
• Fix: Adjusted a few things to try to prevent Bugs from escaping through the Freight Lift ceiling - you know... the one you're supposed to be riding responsibly.

(2024-03-30) Patch Notes v1.3.15
• NEW: Portuguese localization of the game is now available
• NOVO: Ctrl Alt Ego já está disponível em português
Navigate to Menu > Settings > Language to change language

• Fix: Persist grabber state so that items aren't dropped across level transitions i.e. no more accidentally blowing yourself when trying to carry an ether-canister across from one scene to another.
• Fix: Fattened a few colliders around Freight Lift ceilings to reduce chance of physics glitching through them
• Improvement: Particles now help highlight the collectable bug bits in The Assembler level (new subtle visual effect)

(2024-04-10) Patch Notes v1.3.16
Before I list the changes for this patch, let me first announce sneakily here that New Game Plus (NG+) is coming in a major update on 15th April. You'll get a new gravity manipulation ability, there's a new enemy variant, different enemy placements, at least one new shortcut/skips, some surprises along the way, and you can carry over your resources from any existing save.

• Fix issue whereby a previously serialized Bug that had since been reprinted could end up thinking it was still inside DAD
• Fix: Correction to bug grab state across level loads - could end up in a state where it never cleared the grabbed thing
• Fix: Egonomics - Exterior geometry was disabled in the Comms Tower section! Might have been broken since v1.3.0, oups.
• Fix: The Cloud elevators were missing ceiling collider! Also probably broken since v1.3.0
• Improvement: For ultra low VRAM PCs, the game will now run with a very low texture budget - meaning it will look very bad but at least it will run. Anything under 1GB VRAM is considered ultra-low. One player was able to complete the entire game with a mere 128MB VRAM.

(2024-04-15) New Game Plus (NG+) Has Arrived
The full campaign, with a twist:

• New gravity manipulation ability
• New and different enemy placements
• New surprises along the way
• New shortcuts and skips
• Carry over your Ego, Disks, Worms, MEM from a previous run
• All achievements remain achievable

Troubleshooting / How To Unlock NewGame+
If you've completed the main campaign, NewGame+ should unlock automatically when you launch the game with this update. If it hasn't unlocked, try loading up any Chapter 8 save (The Cloud) and that should give it the nudge it needs.

If you haven't visited The Cloud then you're missing out or the auto-unlock isn't working for whatever reason, you can force unlock NG+ like this:

1. Navigate to your Steam apps Ctrl Alt Ego install folder and navigate through to the Ctrl Alt Ego_Data/Scripts folder, e.g. for me it's:
C:\Program Files (x86)\Steam\steamapps\common\Ctrl Alt Ego\Ctrl Alt Ego_Data\Scripts

2. Double click the script ctrlaltego.ngplus.unlock.vbs and if all goes well you'll get a success message telling you NG+ was unlocked.

(2024-04-27) Patch Notes v1.4.18
• NewGame+ Fixes:
- ◦ GRAV key is now rebindable in NG+
- ◦ A CAT in rocket launch area was never coming online
- ◦ The second Virus wasn't showing up at the GOD Dock

• Keyboard Input Bindings
- ◦ Grabber > Upright is now additionally bound to Q (default), which means it's also now rebindable
- ◦ Shift and Alt keys can now be re-bound, and can be used as toggles rather than keep-held-down.

• Fix: Grenade blast radius wasn't always damaging everything caught in the blast due to a buffer not being large enough

• Fix: A couple of inactive guard-rail pieces in Port 666 still had collision enabled

• A MUM in Legacy Systems had turned invisible

• Improvement: Added some fatter colliders to various vent pieces to reduce chance of physics glitching from inside vent to outside them (and so out-of-bounds).

(2024-04-29) Patch Notes v1.4.2
• Bug 22 was refusing to stay on the train at merging station location! Due to a physics change I made a few patches back, now resolved.
• Defragmentation location, added something to the buglock door to prevent Bug22 being able to glitch through the door

(2024-05-11) v1.4.3: ¡Español!
• NEW: Spanish localization of the game is now available
• NUEVO: Ctrl Alt Ego ya está disponible en español

(2024-05-26) Patch Notes v1.4.4
• Fix: Technical issue where downloading your own MUM meant MUM wasn't sure where she was - which led to some erratic elevator behavior and who knows what else
• Fix: A player discovered an unfortunate soft-lock right at the start of chapter 1
• Several German NewGame+ localization corrections

(2024-06-05) Patch Notes v1.4.5
• Fix: Corrected a technical issue with DADs moving between levels - symptom would have been either DAD broken parts appearing when they shouldn't or not appearing when they should
• Change: A technical change to ensure physics and object transforms synchronized prior to saving / crossing between levels

(2024-06-23) Patch Notes v1.4.6

• Added some measures to bring Bug0 back if he's still needed and accidentally gets lost in CRS (e.g. if he glitches through vent)
• VaQ wasn't sucking up Ego Fragments properly
• Download tool wasn't always remaining selected when unctrl-ing Bug22
• Key-bindings screen was not working well for new players / clean install