A lot of the story didn't make sense. Why would any Romulans back Shinzon? If Shinzon and the Remans were enslaved by Romulans why would he want to destroy Earth instead of Romulus? Why would he need a total blood transfusion with 24th century medical technology, if he could be cloned, couldn't the blood just be cloned also? How did he get a ship more powerful then the Enterprise? Its highly unlikely the Remans had the technology or industry to do it themselves so why would the Romulans make it then give it to him?
The script was dreadful. The whole story was an amateurish attempt to make a Star Trek movie without really understanding star trek. It felt like the screenwriter just watched the other trek movies that were considered decent to great and mashed them together.
I'm pretty generous to bad movies, but Nemesis was worse. When I watched it in the theatre (opening weekend), I ended up just saying to myself which other star trek movie the scene was taken from. Here's a small sample (possible spoilers if you haven't seen it)
Peace with a Hated Enemy (ST6)
Captain's Special Archnemesis, Khan vs Clone (ST2)
Riker kicking the guy of Really High Place (ST3) - Kirk vs Doc Brown was better
Disabled Ship Standoff With Bad Guy using Super Weapon (ST2)
Death of a Friend (ST2)
Rebirth of a Friend (ST3) - Hinted at end with B4
Bad Guy can fire while cloaked (ST6)
Special Sense to Smack Cloaked Enemy (ST6) - Deanna's Mind Reading (which she expressly couldn't do according to cannon) vs the Fart-Seeking Torpedo
Deanna Crashes the Ship (Generations)
I've got to stop because I keep coming up with them. Honestly, I'm surprised they didn't throw a couple whales in there.
It was a scotch taped together plot with an excess of CG special effects. In all honesty, the CG special effects were cool.
What I don't get is why people hate on JJ Trek but accept Nemesis as gospel canon. JJ Trek wasn't perfect, but it wasn't the pile Nemesis was.
One of my key criteria for evaluating/rating Trek episodes and movies is how well they stand up to repeat viewings. IMHO the first JJ film actually holds up better than Nemesis did. Hell, the first 12 minutes of the JJ film alone hold up better than Nemesis.
I loved Nemesis when it first came out, but now I consider it to be right in the middle of the pack, in 5th place at best (behind First Contact, Undiscovered, Khan and JJ-Trek).