You can see what's on each at:
http://digilander.libero.it/wedoit/index.htm
http://www.soccered.com/dynamo/contents.html
I think the main differences are the crowd chants, menu screens and music although there are more smaller things.
Dynamo :-
1) Adboards (old-school TheBigK slightly modified by me).
2) CL Ball from WeDoIt2.
3) Boots from WeDoIt2.
4) Kits from all over -- including Korean kits, WeDoIt1 and WeDoIt2 kits, and more. The new England, Ireland, Mexico and Sweden kits are in.
5) 6 updated stadiums -- including the Amsterdam Arena Final patch by footyfan (never actually been released for download until now), Nou Camp, Highbury, Old Tafford, Olympiastadion Munchen, and San Siro Milan.
6) Various Goalie Gloves added to 34 club and national sides. For the full list of gloves, please click here.
7) Flag Removal Patch 1.1 + Referee Kits by Zidane&Figo.
8) New Menu/Replay Music (mostly Queen, with FIFA Anthem for player entrance). Please see my home page for short WAV samples of the music.
9) New Title/Logo/Menu Screens (AC Milan and Luis Figo theme).
Wedoit 3.0 :-
New players database for nationals and clubs teams (totally rebuilt)
- All teams formation data (schemes, kickers, etc.) updated to now
- 6 New club teams [Werder B., Porto, Benfica, Lyon, A.Madrid, Betis S.]
- New uniform kits for nationals and clubs [click here to see the list]
- Fix of all 105 teams uniform numbers/names colors & styles
- Fix of: Scotland uniform front number
- Fix of: radar bullets colors
- New real chants for all the teams
- Edit of grass design for all the stadiums (excepts 3)
although not all of this is true in wedoit. The clubs are the same as original.
The teams are the same in both, but the kits are slightly different.