I'd go for the Strat or a standard Tele for a first build as there is no binding to worry about, which the thinline Teles have. Of the Strat and the Tele, the Strat is probably the most hassle-free, as some of the Tele kits really require the bridge pickup cavity enlarging slightly for an ideal bridge position.

I think a pickup upgrade is worth it, but that's something you can do after you've built it and can decide whether it's worth upgrading. Locking tuners are worth doing on a Strat because of the trem, but as the standard kit tuners are pretty decent, don't really add much to a non-trem guitar except for making string changing just a little bit quicker.