The game falls apart if you dare try any of the side missions. I went through a bout of finishing all of them in rapid succession and that completely ruined the game for me. So much so that I was literally 40 minutes from completing the game and I just couldn't stomach it anymore. It took me over two years to get back to it and finally finish it. 
This is EXACTLY what happened to me and why I got around to finishing it only yesterday.
The sidequests in general outside of a few specific cases like the Bring Down the sky DLC and a couple others are terrible. And the repeating planet layout is terrible. Those are the kind of things that make me think the first game was rushed hopefully...
The thing that bothers me most is...well, first off, I agree with Himuro that side missions on the citadel and other story planets (things like smuggling, etc) are mostly fine. But you have this entire galaxy to explore, right? you'd think that missions taking place in space stations and random planets would be awesome. You get to explore, see and interact with different space cultures, either advanced or primitive, engage if the type of things you see in space sci-fi series/movies. Instead, they manage to take something as vast as space itself and condense all the planets and space stations into four or five locations. The closest you really get to what you'd expect from exploring space is chasing after space monkeys. And that moon mission wasn't good, imo. The only nice part was that it was a somewhat unique location. The structure was basically the same as the others and there weren't any choices. Bringing Down the Sky was alright, but that was a DLC side mission. Even the character specific missions, like finding that doctor Garrus wanted to get was a total snore.
Their approach for ME2 sounds better. Fewer planets to explore but each is better and has an impact on the main game. No more driving around shitty terrain on a shitty buggy. And that's another thing: why were all the planets the same? with the exception of the occasional "lol this is lvl 3 hazard so you can't walk outside." Maybe it's too much to ask, but if different planets had different driving physics because of gravity or atmosphere that would have made the experience at least better. As it was, it was just a color swap.
and I agree that the game feels a lot more solid if you just stuck to the story missions and played it as a 15 hour game.
