The trick in using one of these (PBDDI) for me has been the fact that I first focus on getting a sound I like from my passive bass through my Ampeg alone.
After that, the PBDDI is there to add a couple tonal variations and drive combos to sit in different mixes. It'll do a ton of stuff between the drive, blend and EQ controls, and a little does go a long way. It'll do a mid scoop the more you boost the bass in conjunction with the treble, and it'll do a mid boost if you cut the bass and the treble. I tend to find myself relying more on slight Bass/Treble cutting rather than boosting as I increase drive. That, and finding a sweet blend ratio, I don't have much problem persisting the mids I want. Of course, if scooped mids ARE your thing, it'll definitely do that in spades!
The number of mixes obtainable between my amp's natural tone, the 3 PBDDI settings and the controls on my bass is pretty awesome. And when I need something else on the fly, I flatten the tone controls on my bass, switch it into active and can always seem to find what I'm looking for.
Anyway, Deluxe vs. Programmable. You don't have much more in the way of tone shaping with the Deluxe, but you have more flexibility to store and recall presets, which could be especially beneficial if you use a couple different types of basses. I started with just the BDDI, then got the PBDDI because of different settings I liked using on the BDDI, and now I wouldn't mind having the Deluxe's extra presets and input to go along with a fretless I've been lusting after.