I'd recommend Project Infinity but it is in beta and I am not sure all older mods (with a certain structure) are supported.
BWS is outdated, I cannot recommend it any longer, unfortunately.
Regarding the EE Setup Tool from Roxanne it is an open secret that it's not pulling the original mods but some other versions Roxanne puts up somewhere, some also containing unauthorized changes, and also makes tweaks to EET not everyone might want to have, but it is maintained and up to date, so to speak.
So, concerning automated installers you have the choice between pest and cholera, currently.
I assume you know the BeamDog's forums? There are useful lists there with mods that are compatible with BG:EE (BG EE 2.0 and Siege of Dragonspear Compatible Mods) and BGII:EE (List of BG2EE Compatible Mods). And there is the EET compatibly list, of course. There is always the choice of doing a modded install by hand, and there is also helpful people around who will help with finding the right install order.