From personal experience: It's not worth it (I went from Ivy 40k tuition to state school with grants covering tuition). But I would say this depends on circumstances a lot, and I don't regret my decision.
A few issues that I stumbled upon:
The only problem I can think of is getting LOR's from a professor or a committee.
The school I transferred into required one science letter from the same school, so I had to go in the first semester and talk to several professors quite frankly to get a lukewarm letter. He did appreciate my candidness and the effort I put into meeting him weekly throughout the semester to just talk about classes and interests to get a better idea of me as a person (and used my old transcripts as a reference for my academic ability).
Course transfers work weird. I had to repeat a ton of requirements because most of my old coursework could only transfer as elective, a few didn't even get that much recognition. However, I did talk to the dean of my college and explained my old courses and provided curriculum, etc, and got special permission for most of the courses to knock off enough requirement that I only had to spend one semester longer than I would have if I didn't transfer (Ended up transferring 76 of 98 credits -- so practically lost 1 semester which I took over a summer and 1 course in the Fall). The institution required 30 credits to graduate from it, I had 45, and also needed 120 to graduate and had 121. There was only one additional class I had to take to cover the 120 requirement after getting all the other degree requirements.
Then I also had to adjust to living 45 minutes off campus and deal with commuting without a car. And also get accustomed to all the logistics of the new school that you sort of otherwise learn in the first year or two of college (where to register, get help, etc)
Finally, there is always the question of "why did you transfer so late". Tuition is the usual explanation but some people refuse to believe that and are always like "... yeah, but why did you
really transfer?"
Check degree requirements and how credits transfer, if it all works out fine, and you feel right about it, I'd say go for it. Good luck!
[edit] - As far as applications go, the issue never came up except for being asked "why?" by my pre-health committee, and the adviser made it feel like it really wasn't a big issue. One of the doctors writing me a letter asked the same question as well, but didn't make it seem like it would be an issue. He was just curious, especially since I had so little left to graduate.