On this I could write a book. But let me just give some obvious notes.
A) The look, this awful clockwork machine looking crap. They really look nothing like there Original cartoon counterparts or comic counterparts.
B) Vehicle Modes. The autobots were majorly screwed up by the chevy deal, Bumblebee who should be a beetle. Was always the plucky tiny failure of the team. Every now and then he'd come through but he was always more of a gnat than a threat. If they wanted a Golden sportscar then There's always Sunstreaker who was actually a yellow sportscar. The vehicle modes largely reflected the Personality's of the robot. Changing them loses this element.
C) Jazz. The Autobot's smooth talking second in command talked like a jazz man. Not some low class rapper.
D) To much human focus. Yes the autobots are there to protect humans, but even so humans never appeared as much in the show as there cybertonian counterparts. This over human focus hurt in my opinion.
The only thing they managed to get right were names and a few voice actors. Many personalities were changed and many classic elements were to.
Most Reboots erase elements they consider "Campy" or "Cheesy" but they either don't realize or don't care that they are eliminating a ton of heart and soul from the franchise.
I made myself watch the first movie about 8 months after it came out. But after all the previews and reviews I heard from friends I couldn't make myself watch the second one.
I know I am in the minority. It just makes me sad to see everything I love get stomped on by people who clearly don't care at all about it and just want to play of vague memories people have to make money.
Edit: And for the record I had no problem with spiderman, though they made changes they captured the SPIRIT of the franchise and thats what I am most adamant about.