Confession time:
I'm currently going through my second play session of the ME series. I only got into the series as of May of this year. After spending some time on the forums, I decided to check it out. I'm very glad I did. For all the various faults of the series, I really had a wonderful game experience. As a bonus, Jennifer Hale, Kimberly Brooks and Mark Meer were at Denver Comic Con this year. So I got to meet both Sheps and Ashley less than two weeks after I played the games. I didn't know they were going to be there, but my husband did. He wanted to surprise me and boy he did. 
Anyway, for the ME series, bare in mind that I avoided/blocked out spoilers, and almost never used a walkthrough. One of the only times I did was for the suicide mission, because I didn't want anyone to die. I knew the endings were extremely controversial, but I avoided any mention of them. I wanted to come into the series with fresh eyes.
When it came to the Starbrat and the choice of endings, I was...silly. For whatever reason, I only paid attention to the bright shiny light (oooh, shiny.) So I stumbled into (high EMS) Synthesis, due to my lack of paying flipping attention to where Control and Destroy were. I'm pretty embarrassed about it myself, looking back.
I enjoyed it, but it just felt too Utopian to me. Sure, there was some moments I considered payoffs, such as EDI and Joker becoming the same species (I guess? Can't think of another term at the moment,) so they could love each other more as equals. And also my payoffs for saving the Geth, which I also had a lot of fun with. However, it just seemed too "happy shiny" for my tastes. Sure, things are great for now. Yet, mortal nature being what it is, this whole "we are one" thing will fade eventually. There won't be anymore wars between synthetics and organics, but there will always be cultural divisions. For now, everyone is united, but it won't last. The thing that bothered me the most about that ending was the implication that everything will always be hunky dory.
I haven't gotten to ME3 again yet (just finished ME1 again, working on 2,) but I'm going straight for (high EMS) Destroy. I like EDI, but even she said she would risk her life for Joker. She would understand. The Geth...well, no war can be won without sacrifice. It sucks, because I liked the race, but that's just the way it goes. That ending makes the most sense to me, since it overall changes the status quo the least. I also feel like it's the best way to move the story forward. The breath scene is a nice bonus, but truthfully, it just goes in line with my Paragade Shep that I'm playing. She doesn't want to control the Reapers. She doesn't want to force a permanent union between organic and synthetic, since it really warps any notion of free will. She wants the Reapers gone for good, so Garrus (the LI I'm shooting for) Tali, and the rest of her friends can continue to live their lives.
Oops, this turned into quite the wall of text here. Sorry about that.