Inspired some what by this thread and by my love of games with customisable units (not sure why, I just find the idea fun, despite finding that in most games that utilise it it's a somewhat pointless mechanic).

Are there any non sci fi RTS games that allow this? Like having infantry you can equip with different armours or weapons?

I can't think of any, and the possibilities are certainly more limited when compared to the outlandish things possible in a sci fi RTS but I'm just curious if such a thing exists.

The only one that comes to my mind (and actually one of my favourite games) is Battle in Middle Earth II. You can't equip the soldiers with whatever weapons you want though, you just upgrade them which in turn gives them better weapons and armors. Plus there is the hero editor where you can customise your hero (not only the skills but also the stuff they are wearing in game).

Warcraft 3. If you bought the game on the site battle.net you can dl the setup of the game is DRM free (no need for online activation installed or played solo or lan).

When I read historical I thought you meant like different chariot wheels and such.

World War 3 which is basically the Earth games in a more contemporary setting hence no sci fi but very customisable units.

Don't be so sure, the terrorist faction has the option of throwing rocks. :P

Theres always the great Age of Empires… but I don't know of any customization in those games.

I imagine that may be the closest I'm likely to find though, thanks for the suggestion :)

I didn't think there were likely to be any games that did but I just wondered since it seems reasonably common in sci fi games.

I think your onto something there. It sounds right, and AOE series are highly moddable. Might be a bit more work than OP was interested in, but there are a fair bit of mods which can alter things.
http://aoe.heavengames.com/dl-php/lister.php?category=mods

I haven't played the game, but after a little bit of googling this has come up: The Kings' Crusade

In their Q&A section they say this:

"Q5: What features are you most proud of?
A: First of all, The Kings’ Crusade has a very detailed army management system that is still quite easy to handle. Every unit and hero gains experience in battles. You decide what abilities and skills are improved after each level so you are able to form your units the way you want. Just take two swordsman units – you can make a defensive unit out of the first one, which will protect your archers from enemy attack, and you can turn the other unit into a “killing machine” by training it to deal more damage. Then just send them forward and let them cut your foes into pieces. Sure they will lose many soldiers, so maybe it’s a good idea to hire a healer for them. This way you’ll get very different units even from the same unit types that require very different tactics in battle. Your heroes can carry relics, equip your units with different weapons and armours and hire healers, priests/imams or captains as well."

Not sure it's what you're looking for or even if the game is good (mixed reviews in that other store), but here's the possibility...

While i haven't played the first one, from your description i see at least one major difference as far as base building goes: in BfME2 there are no predefined spots for building; you can build your base's buildings anywhere. If you have played C&C Generals, think of that but in the Lord of the Rings world. In fact, if i'm not mistaken, they are using the exact same game engine.

I was about to mention the same game.  It's a real-time strategy game with RPG elements, developed by NeoCore and published by Paradox, and formerly known as "Lionheart King's Crusade".

Here are some useful videos:

 ▪  Official trailer
 ▪  Gameplay video

The Kohan games plays much like that. Let me explain.
You build a company made up of seven spots you can fill with various units. The first four spots are the front, the two after that support (If you put for example front troops like light or heavy infantry there they will act as the front troops too.) and the last a leader of some sort.

There are some restrictions. Standard troops like infantry, archers, cavalry (There are light, medium and heavy variants though not all factions might have them.) and faction special ones can be put in the front or support spot.
Support units like priest, mages summoners and so on only in support spots.
Leaders like captains and specials only in the leader spot.
Only the four front and leader spot need to be filled so you can make small companies.
Lots of possible combinations here.

The reason I mention this game is how the combat works. The company you create work as a cohesive unit and also the units are separate. So it's quite possible to attack a company on the flank or back to take out the squishy but powerful support units.
Companies have zones of control. When a enemy enters that the whole company starts to attack the other company. When combat starts the only thing you can do is retreat to a spot you chose by clicking somewhere if the leader is alive or route to a random location. If the companys morale drop to zero it automatically routs.
The company and leader if a special one gains experience and special leaders can level up.

So it might not look like it at start but the gameplay isn't that far off from what you want.