What didn't go wrong with Nemesis? Between the script leaking, the lack of marketing, the release date, and the director being completely wrong for the film, it's a near miracle that Nemesis wasn't ten times worse and that it didn't permanently kill the franchise.
As for John Logan and his script, it was flawed, but could have easily been fixed. I really believe that he got Trek, but he tried to throw in everything; the captain's chair, the bridge, the warp core, the ship, and the entire fleet; and no one reigned him in, other than Stuart Baird, but his horrendous editing job compounded the problem by cutting the heart out of the script and film and either alienated the cast to the point they phoned in most of their performances or he simply didn't know how to direct the cast at all.
The Argo scene, I really didn't mind. Captain Picard seemed to have mellowed somewhat over time, even making mild jabs at Riker so for me the scene worked fine and wasn't out of character, but rather showed how he had changed between films. I didn't mind B-4 either. If I remember right, the Juliana Tanner android said something about there being two or four prototypes before Lore. Also, I believe in either an early draft or deleted line, that B-4 spoke of lots of lots of places he had been and how he ended up on the world he was found. As far as Lore goes, he would have been extra baggage. Plus, he had a perfect end in Descent, Part 2 and didn't need to come back. The mind rape scene was beyond horrible. The shuttle escape was unnecessary, but fun. Data's death itself wasn't bad, but lacked emotion and was easily preventable by using a shuttlecraft and its transporters.
As far as Shinzon goes, the writing could have been better for him and the directing too, but I think Tom Hardy expressed his essence well enough. Something that may just be me, but in some ways I feel the Viceroy was the real villain or at least should have been. Shinzon was his own man, but the impression I got was that it was the Viceroy who truly poisoned his mind, who molded him into being locked into his ways, and was subtly manipulating him. It would have been a bit better had the Viceroy not been played as subtly as he was and I blame that on the director, not Ron Perlman.
It also would have been nice had Senator Tal'Aura or Commander Suran been Tomalek instead and Donatra had instead been Sela. For me, it would have been more poignant had Sela been the one shown to have gained a grudging respect for the Federation and finally accepted her half-human heritage.
Anyway, all of this is just my two cents.