I would guess they'll give full functionality from the start, so at least one controller that can actually be used as the basic setup (shell or whatever they're gonna do) will be included. Maybe a slightly more expensive bundle that includes additional attachments and/or a second controller for multiplayer games will be offered too.
One thing we learned during the PS1's reign was that if a peripheral wasn't included with the system, there's a good chance it'll fail (unless it's a light gun). Developers don't want to develop for hardware that hey don't even know the consumer will have, which is why so few PS1 games actually used things like the multitap, especially later in the product cycle. Games that have one-off special peripherals for only that game (or one or two games) just don't sell too well (Steel Battallion, Samba de Amigo, DK Jungle Beat). So there's the possibility that if the Revolution's controller options don't get a strong start and an established user base, later developers won't want to develop games that use them (and it gets pretty expensive to keep bundling a peripheral with your games, and marketing two versions, one with and one without).
Some recent events seem to have bucked this trend; the constant stream of DDR games and clones made dance pads popular peripherals to program for, and newer games like Guitar Hero with dedicated controllers have been pretty popular. This might be a consumer reaction to the apprent lack of creativity in the market, the low point of which was 2004 when it seemed like every game was just another sequel.
And, apparently, Final Fantasy really sucks, I guess.