There will be spoilers, but I'll give you a little warning.
First of all, I loved the game. The whole 'universal ammo,' the UI, and other things that people are griping about aren't that bad (in fact, the universal ammo makes sense in the story). The game was a little easy until you came across the 'elite' people of the game (but then again, I played a sneaker most of the way, and it worked out that I didn't get into major fire-fights). My only gripe? It was too damn fast. I played the first one a bagillion times. Even played it through in december to get ready for this one. It still took me several weeks to get through the whole game. This game took me like 10 hours of total playing time. They really coulda put a lot more into it.
OK, now the spoilers come. If you ever plan on playing the game, just stop reading. If you don't care, lets carry on, shall we?
Biomods were cake to come across, but it helped people who wanted to switch around and experiment. I did nothing of the sort, so I ended up with like 12 unused regular cannisters and like 10 unused blackmarket cannisters.
The only biomod I used a ton was the one I got up front (first place you get mods you can charge up one all the way, and that's what I did). Eye mod that allows you to see through the walls. Think about it. In most games this is a cheat! It isn't expensive to turn on and keep on most of the game, either. By far, this is the mod I'd suggest to anyone.
The other one's I chose were cloaking from robots, and bot domination. I thought this would take the cake, but it really wasn't that wonderful. Running in, taking control of a military bot, hiding, and going f'ing nuts against the evil baddies wasn't that great. The hunter-seekers plasma gun sucks, the military bots missile launcher has too slow a reload rate. Its something I shoulda did without (cause mag rail's secondary fire + eye mod = emp'ing bots before you are even in the room).
The other mods were computer hacking (you'd think this is a no-brainer, but there isn't that many computer's around to hack, so it may be better to get regular cloaking), and walk silently (which is nice for the sneaker I am, but I've heard the run fast, jump high is great for hit-and-run tactics).
Weapons? I never used anything like the flamethrower or missile launcher. Too expensive. SMG sat around, cause I never wanted to attact too much attention, and you can't silence it (but kept it around in case an alarm went off, and I needed to coverfire). Best weapons were the boltcaster (3 shots in anything == unconsious on the floor in a couple seconds. With the glass breaking and silencer modifications), the sniper rifle (headshot from long range if needed), and the mag rail (only secondary fire to knock out any machinery you can see through the walls).
Energy cells were a dime a dozen (and I had my eye-mod on almost constantly). Never ran outta ammo. Never had to use all my medkits, cause you can get (and hold) enough food to heal you.
The only thing that was tough in the game was going against multiple power-armored templars. Illuminati elite were useless, cause you can head-shot sniper them. Templars required a lot of firepower to putdown.
JC Denton was a powerhouse badass by the end of Deus Ex. Now he has a super-AI inside of him. Unstoppable, right? 2 headshots and he's down. They shoulda given him a super-ai script, complete with a full set of biomods. That woulda made you think twice before going against his wishes.
I didn't like the JC Denton ending. Felt like I just created the borg.
The Illuminati ending was alright. At least it seemed like a normal ending to the world.
The renegade ending was pretty cool.
But the templar ending was by far the most wicked. It was also the easiest (cause all the templars on the last level are on your side). The man hanging at the very end of the cutscene... they should have panned up to his face... it shoulda been alex's face (IMHO). VERY wicked... I loved it