well, the primary difference (on both) is the S-1 pickup selection system.

On the Strat, it allows many many more combinations than the standard 5-way switch. with the s-1, you can run many combinations or pickups, either in series or parralel, it allows you to get any combination you could think of on the strat.

I'm not too sure what options the Tele with S-1 offers, but since it already has a three way toggle, I assume it offers varitaions on series and parrallel combinations, and perhaps a few combinations of more than one pickup at once.

I also find the neck more comfortable on the Deluxe models (as far as I know they have a different finish on the necks...or the one I played could just have had a very nice neck...think the necks on the deluxes have some special finish though.)

Anyway, hope that helps.