I'm assuming that a top-end iMac will have a fairly high-powered mobile GPU, just like it does now (ignoring the built-in graphics on the 3770, which will either go unused or be used in non-graphics intensive applications to save power) - non-upgradeable, but equivalent to a bit better than the cheap desktop GPU Apple usually uses as the default on the Mac Pro.
That wasn't true during most of the early reign of the Mac Pro 2010 model. The iMac 2010 era GPU topped out at with a 5750M with 1GB VRAM. The desktop 5770 outclasses that card.
It is true that the 6790M is a bit better than the 5770. But the 6790M came out in January, 2011. The 5770 came out October 2009. Sure give the mobile GPU almost a
2 year jump on the Mac Pro card ... yeah it is going to fall behind. It fell behind just like the Xeon 3500 fell behind the i7 3770. They are from different eras.
There is zero reason why Apple would put "last year" cards in the Mac Pro on this update. Even if the iMac upgrades to Nvidia/AMD latest mobile they likely won't catch the mid-range desktop card Apple selects for the Mac Pro as the entry point.
The only way the Mac Pro would come in lower GPU is if Apple embedded the Mac Pro's GPU on the Mac Pro motherboard. But then you'd have a CTO box that was cheaper than the entry price point and an empty slot could fill with a faster card. That's quite competitive.
My definition of a top-end iMac is a 27" with both the processor bump and the GPU bump, although I might well ignore the internal SSD option if it's still as overpriced as it was last generation (I'm happy to boot from a Thunderbolt SSD if they're going to charge $600 for a $200 internal). Any Mac Pro that can't keep up with that ~$2400 machine is, at least to my way of thinking, useless (unless it costs, say, $1799).
First, it is unlikely the Mac Pro will ever be priced below an iMac. ( at least this full sized version. If they came out with a third Mac Pro offering in a small case with an E3 processor perhaps there would be some minor overlap but I doubt it).
Second, this is one of the problems now with Mac Pro pricing. It is not that the Mac Pro is "gapped" from the top end standard configuration but gapped higher than the top end standard with the "deluxe" CTO CPU/GPU options.
The CTO top end MBP 15" is just as fast as the entry MBP 17". That has nothing to do with the entry, "Good" version, level pricing of both models.
That was not nearly as true before Thunderbolt, when the fastest way of connecting anything to an iMac was Firewire 800. The Mac Pro had huge advantages in disk capacity and there were numerous applications which required specialized I/O that took advantage of the PCIe slots.
Mac Pro still has advantages. Are more folks going to settle for fully pumped up iMacs yes. That's nothing new. The Mac Pro just need to find a few new users with workloads from machines larger than it that it can now reach. For the bulk of the market that the market that the Mac Pro is targeted at many of those workloads will increase roughly in step with the Mac Pro. So the iMac isn't a long term option.
If Thunderbolt completely solves the user's problem those users probably didn't need a Mac Pro in the first place.
By the time you pay $300-900 for that external Thunderbolt RAID box with 4 slots you could have paid $300 extra for the 6 core Mac Pro.
Of course, if you have multiple big RAIDs and the highest-end multilane HD-SDI interfaces, you'll saturate Thunderbolt - but the people running that equipment will be buying 12 or 16 core Mac Pros, not 4 or 6 core models.
There likely are some using the 6 core models. This all started with you saying the 1650 was "enough" to put a bigger gap between the Mac Pro and the iMac. Well it is. It just isn't necessary that it be at the bottom.
Now you are drifting off into a different "path" where the Mac Pro single package model completely disappears. Not likely to happen. The single package and dual package models are likely going to be coupled for a long while.
It would be a very appealing machine to people like me - photographers and other creative pros who'd like to pick their own display, need a lot of computer power, but don't have Pixar budgets.
Hence the Mac Pro entry level priced exactly where it is. Either you find value in picking your own display or you don't. If you do then you'll pick the Mac Pro over the iMac. The relatively minor speed match between the fully customized iMac and a entry Mac Pro shouldn't be an issue if place any significant value premium on choosing your own monitor.
If the $2500 Mac Pro is a laughably bad deal with the performance of an iMac (or a $900 Dell XPS 8500), it won't appeal to that relatively savvy group, but if it is a 6-core (which are always expensive - Dell's cheapest 6-core is a $2000 Alienware), it will sell a lot of units to photographers, indie filmmakers, etc...
Apple sells the iMac for those in the $900 Dell box folk. That's it competitor. If the built-in monitor doesn't work for them Apple is OK with that. As long as enough people buy the iMac that is what counts.
The Mac Pro isn't aimed at $900 Dell tower boxes any more than the $2,000 Dell workstation boxes are aimed at the $900 Dell towers.