1) I work with big files and TM2 is slower than TM1.
This can't be helped at the moment, I imagine that the parsing system has been left to allow for alterations and additions before the final optimisations will be made to bring it up to speed.
2) There are some problems with the preferences of the bundle. I'm not sure if the preferences are used.
3) I can't trash the .aux, . log files
I have forked the avian latex bundle on github, and corrected quite a few issues, including the preferences problem you mention, that have arisen in TM2.
5) with TM1 It's a pleasure to click on xyz.tmproj icon to get a window with all your files of your project. Perhaps I can to do the same things with TM2 but I don't know how !
Yes, though you need to use .tm_properties and favourites.
I have been using the TM2 alpha since its release, and I'm currently writing my PhD thesis - lots of teeing. All in all, it is a great improvement on TM1 in lots of different ways (which far outweigh the slow parse speed when opening documents, at least for me!).
Congrats to Allan and all others involved! Very much looking forward to the official release.
David