I'm no fan of complaint for complaint's sake, but I use both lines. C2C from Upminster when practical, AGA from Brentwood/Shenfield otherwise, since that's actually where I live. Work is on the Jubilee line, so this necessitates using Stratford or West Ham.
Putting aside opinion for one minute, the facts are:
C2C: 8tph 0800-0859 from Upminster - West Ham
AGA: 12 fast tph 0800-0859 from Shenfield - Stratford
Peak adult Oyster fare (including Jubilee line interface to zone 2):
C2C: £2.70 for combined distance 16.4 miles (16p per mile)
AGA: £7.50 for combined distance 21.4 miles (35p per mile)
Likelihood of getting a seat (in my experience) - approximately:
C2C: Cramped seat (centre of 3) 80% of services, Spacious seat (adjacent seat(s) free): 25% of services.
AGA Fast: Cramped seat (centre of 3) 20% of services. Spacious seat (adjacent seat(s) free): 0% of services.
Rolling stock:
C2C: 100% Class 357 - all air-conditioned, fairly quiet
AGA: 95% Class 321, 5% Class 315 - neither air-conditioned, the former quite loud
Punctuality:
C2C: Recorded performance 97-98% on-time, Typical experience 98% on-time, 80% RT
AGA: Recorded performance 93% on-time (I think?), Typical experience 90% on-time, 30% RT
For me, this makes C2C the preferable franchise, due to the considerably lower fares, higher standard rolling stock, higher punctuality and slightly reduced crowding. Neither franchise is perfect, I'd ideally like West Ham to see a higher rate of peak services to/fro Upminster as I often have to wait up to 10 minutes in the evening peak, but this isn't much of a complaint, given I can reliably board a service, and can also expect it to arrive on-time. AGA fast services can usually still be boarded at peak times, but slow services at Stratford frequently leave people behind. Travelling with AGA also requires a 5 minute connection time allowance for every journey as the majority of services typically run 2-3 minutes behind schedule from my experience. Not exactly a catastrophe but still frustrating if you already have tight tolerances on your journey.
The transition from NXEA to AGA has in my opinion solidified the point that changing franchise operator is not all that's needed. While 321s are comparatively unpleasant alongside air-conditioned 357s, they do not give the impression of being end-of-life. If they were all suitably refurbished, even perhaps not quite to the full extent of 448, but at least getting sealed windows, A/C and disabled toilets, they would be fine.
The problem I suspect is really the line infrastructure itself. Train failures do occur, but all too often the issues are signalling/points related, particularly west of Forest Gate. You can't really blame the franchisee for that can you?