I'd contend that one of the reasons why Rail Replacement is considered such an issue is because they tend to happen at the weekends, when more "non-regular" rail users come out to play: it's not day in, day out commuters, but leisure travellers who 'expect' the train to run to the timetable.
Photographing rail replacement recently (buses being my thing), I heard a small group of 20-somethings approach the station, set eyes on the brand spanking new, only delivered two weeks earlier, -73- plate shiny double decker, and exclaim "ohhhhh maaaaaate, we've got to get the f*****g bus". Never mind that the bus was circa two decades younger than the train, isn't fitted with a ticket machine and so new it had barely been near a school working, it was still deemed an issue because it was a bus.
Another recent experience as a traveller: a rail replacement was working on a Y-basis, with one terminus at the eastern end (Rainham, Sittingbourne or Faversham... can't remember the length of the closure) and two at the western end (Strood and Meopham). The journey time from Meopham to wherever allowed for the trains to run to more or less regular times, but Strood is much shorter. Cue arriving 18 minutes before your train, or having to wait 26 (or something like that - more than 20) minutes for the bus. Who thought it was a sensible idea to have a bus leave 4 minutes before a train is due, then have arriving passengers wait 26 minutes, to connect at one end?!?!
It's a combined issue of what the passenger expects (to be able to turn up and get the train at N-o'clock because that's when it ran six weeks ago when they last caught it, so they didn't check anything before hand), to what the bus company can or is prepared to provide (let's be honest... we've all shared journeys with adults whose behaviour rivals that of alleged 'feral schoolkids' - I've shared many a train with sloshed adults returning from a hooray-henry summer jaunt to Whitstable... why would you provide your swankiest coach?) to what the train company can provide (different at staffed and unstaffed stations... why do some unstaffed stations seem devoid of any information where rail replacements stop, or a tiny poster on the platform? Even if they stay up all the time, unstaffed stations should have clear, high-contrast (black text on penalty-fare yellow background) information for all to see - "Replacement Bus stops on Main Street, 200m walk", or "Replacement Bus Stops on Station Forecourt. Some Buses Limited Stop: Please Check Destination with Driver.".
Dispatch staff: I recall in days gone by at my local station (staffed) the platform dispatch staff used to oversee departure times outside, whilst ticket office/gateline staff did their usual roles. That seems to have drifted, relying entirely on staff from the contractor (in this case, Go Ahead) at termini. Where there are 'extra' staff available, why aren't they being used to help passengers on replacement buses?
Tracking is a harder one... with no ticket machine required on the bus, and no physical tracking of the train, it would no doubt be prohibitively expensive to set up. Short of giving the bus/coach a GPS token connected to rail systems, not sure how you could solve that one! There has usually been less of a problem with knowing the way when dealing with local drivers than those from further afield. Again, from personal experience last year, my outward journey was fine, the driver was careful, prompt and actually delivered us early. The return journey, with a different driver from the same company was erratic, uncomfortable, unsure of where to stop and clearly lost. At one point he drove down a road clearly signposted "No Access to A299" whilst looking for the A299. It wouldn't have been so bad had we not stopped a few feet before the roundabout (for the third time in five minutes) for him to presumably read his map. I wasn't local enough to offer help safely - as well as not wanting to attempt to go downstairs as we lurched around like being in a Formula Bus grand prix, but even I can tell the difference between a sign saying "A299" and a sign saying "No Access to A299" and guessing which exit might be the one I wanted!
Of course, there is also a certain requirement on the passenger to check their journey before they travel, and not rely on last week/month/year. If there is a bus, why would you just assume it stops at a certain stop? We have fast and slow trains - why would you assume it's going to stop at every stop. If in doubt... ask!