The GWML is being electrified, different trains being acquired and timetables will be recast to address the expected continued rise in passenger numbers over the next 10-20 years. The current mess where commuters cram onto trains already full that are intended for long-distance travel to the detriment of those passengers for whom they are provided will need to stop. Just because FGW currently seem to be too weak to enforce their own rules on some trains as regards set down/pickup only at Reading services, doesn't mean that that will continue for much longer. On all the main lines into London, the gateway stations like Milton Keynes, Bedford, Woking etc., the pattern of change in recent years has been to keep local travellers off the peak longer distance trains. This avoids the situation where these trains are over-full when leaving London, but then spend the remaining 60-80% of the total journey time carrying fresh air where quite a few longer distance travellers could be sitting.
As far as the cash-cow aspects of the Thames Valley traffic is concerned, SWT, EMT VT all still have as many passengers as they have seats for so why do you think that FGW (or their successor franchsee) will be any different?
Dwell times at Reading will be (slightly) shorter by enforcing restrictions on longer distance services as the train will only be stopping to let those arriving at Reading to get off, - there won't be the sardines packing into the vestibules via the single end doors.
Seeing that you bill yourself as a "Reading Commuter", I can understand that you don't want the be denied access to the nice new 800/801s, but ignoring what has happened on all the other mainlines into London and why, will leave you disappointed when it happens on the GWML. There will be an 'uproar' in the local press etc. etc. but the passengers will still keep travelling on the 387s, a perfectly acceptable train for a 25-30 minute dash.
Trying to compare Reading with the likes of Bedford is grade one apples and pears stuff. There are all of three EMT trains into London between 6.30 and 8am, which terminate at St Pancras, rather than continuing into the heart of the City, so it's not surprising that most Bedford-London commuters are not on the EMT expresses, is it?
Ever so slightly different from Reading, which is, as noted above, very important for inward commuting from the Thames Valley, Oxfordshire and West Berkshire, and one of the most important interchange stations in the whole country. Neither is the case at Bedford or Woking, and while there is commuting into MK, it's no use as an interchange.
Pretty much everything will continue to stop at Reading in future and will be highly unlikely to be subject to all these draconian measures you seem to think will be enforced - unless you know where the army of staff required to do that is going to come from.
I fully expect that GWR will encourage Reading commuters to use the Class 387 services but by rather more subtle and boring means than the sort of thing you seem to favour, such as publicity campaigns pointing out that if they want a seat - one of their most constant complaints - they are far more likely to find one on a 12-car 387 that has just come from Swindon, Oxford or Didcot and delivered a lot of Reading-bound commuters to make room for them than on an 800/801 from Bristol, Cardiff, etc, full of people also off to London.
Once some of them cotton on and spread the word that they will get a seat on a 387 service, I expect a lot of them will happily make the switch - right now, where the choice is basically a busy HST from/to somewhere further west, or a trundle along the reliefs on a Turbo that is bound to be rammed east of Slough, it's hardly surprising they all pile on to HSTs.
