Being a regular GEML user, the 321's and Mark 3's are just the right stock in my opinion for the line, they just need a refurbishment! Watch out for 321448 emerging from Doncaster soon... But in my opinion, do the following and you're sorted:
Refurbish the 321's with 2+2 seating and a DDA toilet in the DTCO. Rip out the toilets in the TSOL, which gives a TSO, an MSO and DTSO just for standard class seating, nothing else. by my reckoning, you would only lose about 30-40 seats per unit which are quite often not used as a lot of people don't sit in the middle seats of the bays of 3. As for the Traction Package, it was ruled not cost effective to re-do the SWT 455's which still have EE507 motors over 40 years old, so I doubt you'll get new traction packages to replace 24 year old Brush Traction motors. Just overhaul them heavily and the bogie's too, and you're good to go I think. No need for A/C in my opinion either, expensive, space consuming which there might not be enough anyway, and even on hot summers days the hopper windows provide plenty of air!
Overhaul the Mark 3's as Chiltern have, new seats, DDA toilets, retention tanks and plug doors, get some TRAXX's to run with these, and new DVT's. There's a bit of a cascade opportunity here too. With the 5 360's from HEx being redundant soon, bung them together with the 21 FGE units, make 'em up to 110mph and deploy them on the ECML and deploy them on the residual peak-hour semi-fasts post-Thameslink. Cascade the 12 317's, and the 13 321's back to Anglia. With LM eventually getting the 350/4's from TPE after a few years, you can displace the 7 321's here, over to Anglia too. The 20 321's replace the 20 diagrammed 360's with a shortfall of one set which I'm sure can be made up. The 12 317's go to West Anglia along with the 9 317/7's, which can replace the 18 or so 315's in use on Enfield and Chingford services. This provides the whole fleet of 61 315's which can be moved onto the Valley's or wherever they are needed. There might be around 3 317's spare once you've taken this into account, so you could diagram a triplet on the GEML in the peak which allows 3 321's to strengthen elsewhere.
With this plan you get one fleet for the GEML outer-suburban services which are fit for purpose and inexpensive to keep going, and I'm sure you reduce maintenance costs and diagramming complexity and train-crew competency issues by having just one fleet. Same with the WA by eradicating the 315's, and you do this all and providing a little extra capacity for a fraction of the cost of ordering new trains!