So I got to the end after doing EVERY quest in the game (86 hours roughly), I finally got to the end (renegadely). 
 

illusive man is going to use the tech to make humans the dominant species of the galaxy.

Nobody really knows... all speculation right now.  I guess we'll see in Mass Effect 3 how all these big choices really change the outcome of the story. 

No, it doesn't mean that. 
 
The view of the reapers coming towards the galaxy at the end happens regardless. It's just showing that the reapers have a massive, massive armada, and they are coming to our galaxy the old fashioned way, since opening up the citadel didn't work, and their plan to build a new reaper in our galaxy (presumably to try and retake the citadel) didn't work either. 
 
Saving the reaper tech will likely help you in some way in the third game, but there's been no evidence that the illusive man is evil to the extent that he'd help the reapers, though it's quite possible he uses that technology for the 'advancement of mankind'.. Just keep in mind his lines, such as "Cerberus IS humanity" :P

" @demontium: Its implied that he might use it for his own agenda "

The Reapers are seemingly just trying to fly from deep space to the galaxy and do their whole "kill every organism alive" plan.  How they are able to do this is unknown, as ME1 has told us that the Reapers needed the Conduit in order to reach the galaxy.  Harbinger did say  though right before the Collectors died from the blast that they "... will find another way."
 
TIM is planning to use the advanced Reaper tech to fight any potential Reaper attacks.  Also, considering Cerberus' past, it is likely that he will use the tech to force human dominance over Citadel space.

" I think the choice will only affect the cutscene at the end of the game, some dev said ME3 won`t take as long to develop as 2, which probably means they won`t have two practically different games (you working with the illusive man the whole game, or you working by yorself) in the works.  "

Well, sounds like we all just have to wait for ME3, great game though.

It is implied that the Reaper threat (which for two games now has been referenced) is coming.

Dude 86 hrs?  I got 2 playthroughs in with every quest in around 60hrs.

" Dude 86 hrs?  I got 2 playthroughs in with every quest in around 60hrs. "

86 hours is a lot. I took 40 hours for one playthrough and I think I completed nearly everything, including scanning every planet that registered as "Rich" - I skipped the rest of them and still ended up with way more resources than I needed. Yes, I purchased all the star charts, did side quests, investigated every anomaly, all of it. I'm sure there are a few things I missed, but I'd say I did 90% plus.

" @Skytylz said:

" Dude 86 hrs?  I got 2 playthroughs in with every quest in around 60hrs. "

26 hrs of planet scanning. "

Before you blew up the ship, Harbinger the Reaper was controlling a collector in that ship and activated the alarms to wake up the other Reapers.  So at the end you see a mass invasion of them coming into the galaxy.

" So I got to the end after doing EVERY quest in the game (86 hours roughly), I finally got to the end (renegadely). "

How in the world did it take you 86 hours? It took me about 30 to every mission in the game.

"No, it doesn't mean that.  The view of the reapers coming towards the galaxy at the end happens regardless. It's just showing that the reapers have a massive, massive armada, and they are coming to our galaxy the old fashioned way, since opening up the citadel didn't work, and their plan to build a new reaper in our galaxy (presumably to try and retake the citadel) didn't work either.  Saving the reaper tech will likely help you in some way in the third game, but there's been no evidence that the illusive man is evil to the extent that he'd help the reapers, though it's quite possible he uses that technology for the 'advancement of mankind'.. Just keep in mind his lines, such as "Cerberus IS humanity" :P "

" @demontium said:

" So I got to the end after doing EVERY quest in the game (86 hours roughly), I finally got to the end (renegadely). "

Oh god, 86 hours? Did you spend half the time staring at a wall? "

" How in the world did it take you 86 hours? It took me about 30 to every mission in the game. "