I think those ideas are a little misplaced:
1. Six coach trains into Waterloo in the peak, no matter where they come from, are a waste of track capacity.
2. Basingstoke to Reading would be better linked into express trains to Paddington than having through trains to the North Downs Line (although the Paddington train idea requires electrification from Reading to Basingstoke). I don't think the layout at Reading does lend itself to through trains through platform 7 between the Basingstoke and North Downs Line. Are you suggesting that people would travel on direct trains from Basingstoke to Gatwick. That is not a quick route.
3. There would still be the potential for TOC on TOC delays at the east end of the route. Is it important to eliminate TOC on TOC delays? What problem does this solve?
4. Even if (diesel) stock could be stabled at Guildford, it would still need to run to a depot for servicing - are you suggesting they run to Salisbury for this?
5. Early arrivals and late departures at Gatwick are key and passengers use the line to connect at Reading. Indeed, you can argue that it is most appropriate for FGW to run the trains because of the connections into trains at Reading.
While it remains a diesel route, it is appropriate for the North Downs line to be run from the Reading end by the Great Western franchise with some stabling at Redhill.
Well as someone who knows the patch and has lived and worked on it for nearly 50 years, I think I have more than enough experience to know what's what.
1. 6 car trains are NOT a waste of pathways, they're an integral part of it, there are several in the AM/PM peak times and it is always better to a 6 car train than a 0 car train, also you seem to forget that the maxima for the SWT patch is 10 coaches when it comes to 158 & 159 trains.
2. SWT could easily run a couple of morning trains up to Reading as 3 cars, bring them back to Basingstoke and attach to an Up London either a Salisbury - Waterloo or even the 6 car 159 set that originates in Portsmouth, whilst it's not going be the fastest, it would enable passenger from Bramley or Mortimer to have a seat, rather than fighting for one with the hoards at Reading.
As for creating Basingstoke - Gatwick as a direct service & saying it's not a quick route, you can say that equally about Southern's dreadfully unreliable Southampton - Gatwick (Victoria) service, that's just as bad.
Anyway, if you have a load of luggage & kids behind you, you want ease & simplicity and minimal changes of trains, creating a Basingstoke - Gatwick service would do that for passengers coming up from stations on the Salisbury line, as well as Winchester, Fleet etc.
These units could be provided from Salisbury after being serviced.
3. You seem to have forgotten that with the new layout at Reading, there will be a direct route from the from Oxford Road Jn, Cow Lane Jn, under the mainline to Platforms 10 - 15, with platforms 14 & 15 being the best options as the provide easy access to the reinstated dive under just off the end of those platforms.
4. What I am on about is by removing FGW from the equation, you get one less TOC on TOC delay (TDA has a lot to answer to in my mind, a 5h17 idea), by giving the North Downs line (I'll refer to it as NDL from now on), it eliminates a double whammy of delays.
For example, at the moment a FGW late runner impinges on SWT & SN and possibly FCC (TGSN as it will become).
Remove FGW and it becomes SWT on SN & FCC (TGSN), it is simply removing another layer of wasteful bureaucracy from the system, less paperwork, less managerial/back room staff needed to argue whose fault it is, so money saved in all departments, which is good thing.
Anyway the line will become integrated into Basingstoke ROC in the next 3 or so years so you might as well keep it within the deep alliance, so operationally it would be prudent to keep the whole lot together.
5. FGW to be quite honest couldn't & quite simply cannot run a decent service across the NDL, it's regularly late and it's one of the primary causes of delays on SWT's Portsmouth mainline services, the 0434 is one of the worst performers going, even after they retimed it, it still misses the connection into the 0514 to Waterloo at Guildford.
In my experience SWT has a bit of reputation for sorting out bad running trains.
The first trains can be berthed at Redhill, nothing to say that SWT crews could not do night work and stay with the trains overnight either at Redhill or Gatwick or if necessary run ECS from Guildford to either Redhill & Gatwick or Reading.
You may say that is a waste of money, but SWT already run ECS from Salisbury to both Yeovil Jn & Axminster each weekday morning, rather than provide a depot & fuelling point say at Exeter Central or on the former depot site at Exmouth Jn. Guildford to Reading & Redhill is a short hop by comparison.
Better still when the franchise comes up for renewal, integrate it into the SWT franchise, but a part of the franchise is that the franchisee has to electrify the NDL, but in return they get discounted new rolling stock & help to fund any necessary platform extensions, which would seem to be a reasonable deal for long term growth.