I'd just like to say that I am finding this discussion fascinating. I work in timetabling for a very different kind of transport (which is also done manually, but with more and more computer modelling to help us optimise), so it is very interesting to see the challenges that you face.
The above quote does sound like an area where better software could do a much better and quicker job of testing the timetable than what you describe. I would have thought a decent semi-permanent model of the way the network works could have been built up fairly simply, that you could 'simply' upload a full national timetable into (and ideally also things like staffing rotas), push go, and have a decent set of answers come out of the end to flag up concerns, and perhaps also suggest potential solutions.
That is effectively what RailSys can do to some degree (other than the staff and recommending solutions part). Trouble is that big national models take *huge* amounts of computing power, manual update/checking and manual analysis of the "concerns". Just maintaining and keeping up to date such a model is an expensive cottage industry in itself!
The trouble is, of course is that any area of performance challenge is not necessarily just for the timetable to resolve. If anything, changing the timetable should be the last resort.
Take an example like East Croydon or Clapham Junction. You don't need to run a RailSys model to tell you to expect reactionary delay between trains calling one behind the other as a result of dwell time variations. So your options are:
1. "Change the timetable", which at these locations almost always means taking trains out. This then creates a circular problem of putting remaining passengers on fewer trains, and creating dwell time problems either here or somewhere else, or perhaps tightening trains at another junction.
2. Make the current timetable work better: i.e. you use the outputs of RailSys to focus on basic stuff light getting dispatch procedures right, stopping positions in the platform, signallers setting routes promptly, clear plans should trains get delayed in the platform etc, so that there is less variation to dwell times in the first place
3. Infrastructure: even simple things that can be fixed in relatively short timescales, e.g. are the OFF indicators well-positioned, is the TRTS/RA button in the optimal place on the platform.
The first course of action should always be "can the current timetable work better?" rather than "lets mask what is sub-optimal by changing the timetable". This is like comparing apples and bananas; RailSys forms part of, but not all of, determining the actual answer.
The network model could be continually updated with actual performance data, so that it 'knows' that TPE are likely to skip-stop if a train is more than 10 minutes late (for example), and how many people are likely to be on each train, but it could also be 'curated' to manually create realistic days with a range of elements (from speed restrictions and broken down trains, to events causing extra crowding etc), that could be kept in a library to allow every new timetable to be tested against them.
Regulation/recovery strategies and passenger loadings themselves have a circular relationship to the timetable*, as well as being influenced heavily by performance regimes. e.g. delay may be minimised overall by cancelling a train, but the TOC will not do that if that results in a net greater financial penalty, and the relative incentives may vary through the life of the franchise. It's often perverse, but it's reality.
*Good example: Since, May 2018, the 1Txx King's Cross-King's Lynn services have been more commonly known to pick up calls at places like Hitchin during disruption to other services, as there's a bit more natural 'slack' to take them up. Pre-May 2018 you generally wouldn't have done, as it would have messed up the King's Lynn single lines too much.
Perhaps RailSys already does this, but it doesn't sound ideal - it sounds like a task that could take a few days rather than a few months with a decent tool, leaving more time for the timetablers to do the creative work of building the new timetable.
RailSys is itself interesting work when you get to the analysis part; going through data, picking out trends, drawing conclusions, making recommendations. Even sitting with actual signallers playing through example scenarios!