At present, BG:EE is still using the SoA familiars, sans the BG2-specific dialogue. I'm working on rebalanced BG:EE familiars that Tutu is more than welcome to use.
You can examine BG:EE files using the latest NearInfinity. I don't know where you would find a listing of what was changed, but you should be able to compare descriptions of the spells and classes/kits to their BG2 incarnations.
It probably wouldn't be terribly difficult to re-implement these changes yourself, especially if you have some patience and a reference on how to do what you want.
The BG2 spells and abilities were probably not intended to be used much by level 1-7 characters, so they aren't necessarily very well balanced in Tutu/BGT. One of the goals of Kit Revisions (in progress) and Spell Revisions is to ensure things are balanced at all levels, including the early levels in Tutu/BGT. If you have any suggestions, feel free to comment over on the G3 forums.
I was reading about BG:EE and saw that Find Familiar, Shapeshifters, and Totemic Spirits had all been nerfed so they were no longer overpowered. Is there any project out there that addresses these three issues for Tutu? I know that TutuFix tried to fix totemic druids (although this wasn't properly implemented). If not, how hard would it be to mod the files myself to align these with the balancing in BG:EE? Thanks!