My experience is Vienna is limited to a half dozen very short stays over a lot of years; and it reflects how I do things which may or may not be useful; so, don’t take any of this to the bank.
Day trip to Bratislava: For me, for a major city like Vienna, 4 nights is the minimum for a first-time visit. I would need that much time to determine if I loved it or was bored with it. So conceivably I could work in Bratislava or elsewhere. I did that with Bratislava last year. Even spent the night in Bratislava which resulted in me being there the better part of a day with a guided tour, and the early morning the next day, before moving on. In my case I went on to Gyor and the Archabbey at Pannonhalma (time much better spent than Bratislava for my interests ... despite being a repeat visit), then Budapest. Wasn't impressed at all with Bratislava (except for the UFO. Dont ask me why but that place really spoke to me. Spent a few hours there).
An apartment with a kitchen facility ... We don't want to stay too far
off from the main area:
I won’t lie to myself and say that I am going to cook on holiday, so I can’t be helpful with the kitchen aspect. I do order pizzas on ocassions or bring home KFC. I also don’t want to be too far from the main area. In Vienna, for me, that means being in the Ringstrasse or within a 3-minute walk of it (south to southwest side of it). So far none of the recommendations you have gotten would work for me. I have been on the metro in Vienna, and I will confess that it is incredibly efficient … I don’t want to be moving efficiently underground on my holiday. Just me though. Each trip to Vienna I have resigned myself to the fact that my hotel was going to cost $250+ each night if I was going to have the sort of holiday I most enjoy and value. Hence short trips.
Finally, I guess for me the question requires context with the other stops. For my interests Prague would be 3 to 4 nights. Probably 4 nights if it’s the arrival city from the US. Day trips would add a night for each trip. I wouldn’t do Cesky Krumlov as a day trip; that’s a stopover on the way to Vienna and it gets a night or two. Remember just my taste, there is no right answer to any of this.
Vienna, for my interests, and if it were a first visit, 4 to 5 nights. My son loves museums so if he were with me it would be 5 nights in Vienna. He would be in the museum, I would be in the museum cafe. Without him, I would stop at 4 nights and move on or maybe do a package day tour drive up and back to Melk. All the other stops and maneuvers (river cruise, etc.) related to Melk don’t light my fire compared to spending the time in other places and other things in the region.
When it comes to Budapest, I am a bit biased. But most will say 4 or 5 nights. Sometimes it is about what it physically takes to do the job. In that case the tourist area or old town if you want to use that phrase, in Budapest is literally 10 times the size of the equivalent in Vienna or Prague. Sometimes its about what interests you and what you enjoy doing on holiday. I ended up living here because this place ticks all the right boxes for me. But trying to be objective 4 or 5 nights and that will get you one day trip or a half day trip.
Sometimes it’s about what’s going on in the destinations. For Budapest in September, you have great choices. One of the best months to visit. Might be the same in Vienna and Prague too, but I just don’t know. Here are some ideas and dates and the link to more https://community.ricksteves.com/travel-forum/hungary/updated-budapest-events-for-january-june-2026. I know that link, and links for apartments and hotels and performance venues is on one of your other threads. So I wont repeat.