Uh, the main quest IS just something like side quest, IMO.
The emperor: "Go find my heir ASAP or everything is lost!!!"
You:"Whatever, dude. Just lemme explore some ruins for some nice armor/weapon. Then I'll become champion in arena. Then I'll become master thief. Then I'll....."
I know, it is about freedom and such, but the storyline feels so.....weak.

Yes and what Enhanced Deadric Invasion does is make it seem more like there's an actual invasion going on http://www.tesnexus.com/downloads/file.php?id=9858

You either follow a linear path given by the game, forcing you to follow the storyline or you let the player do it (or don't at all) when they see it fit. That's the whole concept behind an open game world.
And I can't think of any game who achieved to combine both, without letting the storyline feel a bit like a sidequest. San Andreas would probably come closest, but only with forcing you to play the story in a much more linear way and restricting areas.
Besides, that's the beauty of games like Oblivion - there are mods who add more and more consequences the longer you neglect the mainquest. So don't blame the game just because you where to lazy looking for it. :)

Thanks - I do own Oblivion just haven't played it yet. Still waiting for the FO3 Game of the year to drop in price.

I totally agree.
I think I ended up with 250+ hours of playtime on Oblivion after installing Oscuro's Oblivion Overhaul (OOO) Mod (which added tons of new content as well as fixing the auto-leveling enemies) and a level-up mod that made the way one levels up more intelligent to me (I forget the name, but there were several last time I looked).
I ended up with around 100 hours of play on Fallout 3, and I never finished the NE quarter of the map. I kept planning on getting back to it to finish up some things, but I always found something more interesting to do instead. I'll refrain from mentioning which parts I wanted to get to but never did, as I don't really want to spoil anything. I will note that I never used a mod for Fallout 3 (I lost interest before most came out), so that might have made it better for me; I truly doubt it however.
EDIT:
Those playtime numbers I listed are for just one play through each. So, Oblivion gave me 250+ hours of playtime with the same character. Fallout 3 would have probably been around half that if I had finished everything up like I did in Oblivion.
It is somewhat apples/oranges though, since I had a content mod with Oblivion, and no mods with Fallout 3. So, keep that in mind.

It wasn't so much a matter of copy/paste in location design (many areas actually had fairly unique and memorable designs), but rather that the heavy use of leveled lists and lack of hand-placed, static enemies and items ensured that the locations had no real character to them. Once you popped into a dungeon and saw what enemy type inhabited it (bandit, undead, goblin, beast, or daedra) you knew exactly what you'd find in the rest of the dungeon. Basically you'd have the same experience whether you explored every dungeon in the game or just ran the same 5 dungeons again and again, and this realization really killed any thrill to exploring the game world. Fortunately this is one area that Oscuro's mod did a very good job of improving on.

Both are great games.
OBLIVION: medieval fantasy
Pros: LOTS of quests and side-quests, good atmosphere, factions to follow, decent playability, graphics, etc. Many friends of mine regard it as the best medieval fantasy RPG ever created, I disagree, but it's still a good game.
Cons: the difficulty for magic-driven characters is disapointingly high because they're underpowered; the world could be larger (you can see several cities from the same spot in certain high mountains); close-combat doesn't feel so right in first-person games (IMO); enemies level up like you, so random road-side thieves come wielding magic weapons from a point on. The main quest is slightly boring (all "portal" dungeons look alike).
FALLOUT 3: post-apocalyptic
Pros: just as many quests and side-quests as Oblivion (you'll never run out of work); great atmosphere, cool dungeons, fun first-person shooting, cool items/equipments/fixing system/crafting system, larger world in comparison to Oblivion (less cities though); nice free-style gaming (you could forget the main storyline and still have a lot of fun).
Cons: main quest is extremely easy, short and not very rewarding. This is a defining point of the game. It takes you exploring about 20% of the map to complete the main story, which leaves a strong taste of rushed-out-the-door-game in your mouth. If you take the time to look for subquests and explore the map instead of pursuing the main quest most of the time, it's much better.
I favor Fallout 3 mainly because the game is more exciting most of time and the Oblivion cons spoil the game for me. Oblivion begs for third person fighting. Fallout 3 main quest problem is serious, but as I said, you should explore the map the get the best out of your game. Also modding Fallout 3 can turn the game into a much more intense experience.

I prefer Fallout 3. I'm not particularly interested in Tolkien style Fantasy.

All true :)
Choosing by genre here might be a good idea. If you're distinctively into one genre over the other, you probably have a winner.
They do look alike. I think the Fallout combat animations and enemies look better.

I think it's *very* harsh to accuse one of the few good modern post-apocalyptic games of "no uniqueness"; it's far easier to see that in any medieval fantasy, specially one with a save-the-world-from-hell storyline like Oblivion. Also, come on, everything being hard to come by is the whole point of Fallout, if you like Doom-style dropping, play Doom instead! That said, it's important to agree that modding these games is near-mandatory, and everything else you said I can agree too.

Nothing will make you run backwards more than creating a magic user in Oblivion. Play a few rounds in the arena if in doubt! In Fallout 3 you can run and gun as any FPS, you just need balls (and saving often). ;) Relying only on VATS is a common mistake in this game.

VATS is really overpowered. When you reach the lvl cap you can basically kill anything even a large group of people without firing a shot outside VATS.

Yeah, and the Grim Reaper's Sprint perk pretty much makes it a joke. Once I got that, the game just became an endless stream of VATS headshots.

Sniper perk, grim reapers sprint and full energy weapons kills anything even a super mutant behemoth if you have the alien blaster without leaving vats.

Amen to that, on top of the superbly bland landscapes comes the dialogue which is, at it's best, poorly delivered and incredibly uninspiring.
Massively overrated game.
Not played Fallout 3 at all but I intend to give it a try, I'm a huge fan of both the previous RPG's and the Tactics spin off but the fact that Bethesda, with their poorly animated worlds and piss poor dialogue, got a hold of the series causes aprehension. :(

Get FCOM and some magic overhaul mod for Oblivion... You won't even notice you're playing the same game.