By just looking at the standard machine (not taking into account any addons like an accelerator or Picasso-IV) I will still vote for the A3000.
To modern day standards the SCSI-I is slow, true, but that's not what retro is about (and to me, Amiga is retro, and not competing to any modern day computer).
The only advantage of a standard A4000 are AGA and easy memory adding via SIMMs (which was just as expensive as ZIP ram back in the days), but AGA has not much of an advantage over ECS when you use it as a productivity machine (which they both are - want to play games? buy an A1200!). Who needs a 262,144 color Workbench when you're coding or writing some documents?
As for the tower versions and expansions: sure, the A4000T has faster SCSI, but when you add a Cyberstorm and/or Picasso, you must do that to the A3000T as well to have an honest comparison. Result? Still not much difference between the 2, apart from AGA, which you don't use much with that Picasso installed anyway. 2 video slots? Nice, but people who don't do any video-related stuff on their Amiga aren't likely to have much use for it.
The cases in overall view indeed again: each to his own taste. I find the A4000D very boring, and the A3000D very pretty. The A3000T might be a heavy beast with lots of screws, but at least you can take a side panel off without the need to topple the machine over because the A4000T's side panel also includes the top and bottom side of the case. But then again, I find the looks of the A4000T nicer than the A3000T (which looks a bit too massive)
Conclusion:
I would choose the A3000 when it comes to desktops and the A4000T when it comes to the tower versions. Any comparison between an A3000D and A4000T (or the other way round: A3000T vs. A4000D) is nonsense in my opinion. As for functionality, it's almost a tie between them. Like I said: you don't buy an A3000 or A4000 to play games, so please don't mention AGA. The only useful program that I know that uses AGA is DPaint.
End of rant. I'm now going to think happy thoughts again :-)