Taking a trip to southeast Asia in May, arriving in KUL on a Thursday afternoon and departing BKK the next Monday evening. I don't have any hard constraints on my time, but I'd prefer to spend at least one full day in BKK.

Given my flexibility, I've done some looking into taking the train from KUL to Penang to BKK. Most of my information comes from seat61.com. Seem interesting (and isn't very expensive!) but I've read some dismissive comments online, generally citing old equipment and not much to see, and the fact that it's much slower than flying. I have looked into flying to Penang and taking the train from there, which saves several hours of travel time and is fairly close in price to just taking the train (and with this option, I'd take an overnight in Penang as a buffer, and thus would get some time to explore).

Does anyone have experience with the train in Malaysia/Thailand? Is there anything that I'm missing or not fully considering?

I'm not sure how familiar you already are with BKK, but if you haven't been there before and are not a train nut, I would most definitely recommending flying instead and spending the extra time exploring the city, and daytripping to Ayuttaya or Kanchanaburi or something if you want to get your SE Asian train kicks.

Malaysian & Thai trains are at best functional, it's a slow and not particularly comfortable or exciting ride. Even the fastest possible connection from PEN to BKK is ~24 hours, or almost 12 hours extra if you go all the way from KUL, whereas the flight is only a bit over an hour and costs peanuts on Air Asia & co.

Take people's advice an fly. AirAsia flies direct route, it is two hours and if booked in several weeks in advance, it is just $60 for mid week and $100 on weekend one way.