Top 5...

[Tuor in Gondolin]

I actually like the way Arwen was used in FotR as a
sort of ZenaArwen (rather sexy and gave her more to do and generally
kept Glorfindel's actions intact). But minus points for not having Frodo speak to
the Black Riders at the Ford of Bruinen:

By Elbereth and Luthien the Fair,
you shall have neither the Ring nor me.

Five worst bits
1) Gandalf physically assaults the Stewart (against the specific
ban on the Wizards interfering (see Unfinished Tales).
2) Screwing up my favorite LotR character (Faramir).
3) The Green Slime at the Pelennor Fields (makes pointless the
whole charge of the Rohirrim which, of course, was probably why
Tolkien limited the Army of the Dead actions).
4) The inept way PJ portrayed the charge of the Rohirrim. Instead
of in broad daylight it should have been like the book, start it in
dark, have Theoden give a bit of his book speech:

Arise, arise, Riders of Theoden
Fell deeds awake, fire and slaughter,
Spears shall be shaken, shields splintered,
Ride now, ride now, ride to Gondor!

He takes horn from Guthlaf and blows on it,
then charges ahead of the Eotheod as the sun begins to
come out and shines brightly on his shield.
5) The ridiculous way Merry and Pippin tricked Treebeard into
going to Orthanc. Why not have the ents vote to go there
and recite their marching song en route?