Fares
Generally good, and I would say better than the rest of the UK on the whole. I've certainly never been priced away from Scotrail off-peak trains. Advance fares generally have poor availability, but I'll often buy the affordable Off Peak flexible tickets instead which are still good value traveling solo (I haven't bought a Scotrail advance in years). Greater Glasgow is excellent value for money, although I'm sure it's still subsidised.
Punctuality
On the whole, good. When I used to commute in Glasgow, I was only late on a handful of occasions relating to adverse weather. Most routes are often self-contained, with relatively little competition from other TOCs/FOCs which must help. Of course, there is potential for delays on rural and remote single track lines - this can be an issue between Aberdeen and Inverness with a relatively busy timetable on a predominantly single track line, for example. I wouldn't worry about reliability if I was a commuter anywhere in Scotland.
Overcrowding
In general, nowhere near as bad as London. My experience in Glasgow is that loads are generally acceptable providing that the trains run with the number of carriages booked. Longer distance services can be busy on Sundays in particular, but it's often as much an issue with luggage volume as it is with passenger volume. I'd say I almost never failed to get a seat in 5 years of commuting in Glasgow.
Cleanliness
Acceptable throughout. Some passengers seem to be unaware of how to use a toilet, but that's not an issue unique to Scotrail by any stretch of the imagination.
Catering (where applicable)
Acceptable snack service on longer distance runs, sometimes with poor availability outwith standard hours (this is particularly true on Aberdeen-Inverness, where commuters travelling towards Inverness in the morning have no trolley service on the 2.5hr run). Not much beyond a basic snack service, but none of the journeys are long enough for that to be a problem. If it were to be improved realistically in the short term, I'd suggest that a better range of sandwiches and light lunches (salads etc) be made available.
Use of appropriate stock
Generally appropriate. The majority of their trains are commuter services serving the Central Belt, and I'd say stock is probably superior to what you'd find on similar routes in England (156s/158s vs pacers, for example). 170s on long distance runs cause some consternation. They actually do the job pretty well, but as I touched on before often have insufficient luggage space. Worst trains would probably be the 320s, which should give you an idea of how good things are.
Scotrail is generally a good TOC, and I have little to complain about. My biggest gripe is the frequent cancellation of seat reservations on longer distance routes. I'm a satisfied customer.
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I have a sort of related question that doesn't really deserve its own thread. But how good are they at keeping connections out of Inverness between the branches and the highland main line?
I've seen them holding trains to both Aberdeen and Kyle for a delayed Glasgow service (guard phoned ahead to INV with numbers en route). That wasn't a very long delay in all fairness. Of course, it's a balancing act. The services in the Highlands are infrequent, and holding connections is generally a good thing for customers. It may be several hours before another train comes along. Of course, holding the train will annoy passengers from Inverness, and may cause congestion further up the single track line which could cause residual delays for the rest of the day if you're unlucky.
I've found communication for tight Inverness connections to be excellent, given the rural and remote nature of the routes. In the instance where they held a connection for me by about 5 minutes, we were told what platform to go to and had station staff on hand directing passengers so that they could get a good balance. Top marks on that occasion Scotrail.
