I think it would be a nice bonus if they included some remastered deleted scenes, but I think I'd prefer to see the episodes as they aired.
One nitpick I have is how Encounter At Farpoint is broken up into Part 1 and Part 2. When TNG premiered it was as a two hour episode. I would really like to see the show presented as one long episode rather than as a two-parter. How is it presented on the DVDs?
I don't know, but I figure it would be the two hour episode version on the remastered version.
As far as I recall all home video releases of the pilots and double length episodes were in their original 1 episode presentation. The only exception are episodes that were shown in two parts on their first broadcast. Therefore, I'm confident the blu ray releases will follow the same format.