Honestly I think it makes a lot of sense that they're cheaper than an F100, especially if you have mostly autofocus lenses- it's really no contest in terms of usability there. All Nikon SLR prices are low right now, I don't think the F4 is a standout there, I recall them being fairly cheap a decade+ ago, too. They offer more functionality compared to an F3, but I think they're a lot less collectible, for whatever reason- it's rare to see anyone waxing poetic about the f4, and are heavier in any configuration, unless the F3 has an MD4 attached. I have both, but mostly reach for the F3 myself, and if I had to keep one, that's what I'd keep- the F4 AF is too limited to be useful, and it's ideal use case (in my opinion- fast shooting with MF lenses to take advantage of all it's exposure modes, matrix metering, superb finder, and motor drive), isn't something I do much anymore. I don't think their LCD issues are any more common than on the F3, and they don't have the dreaded "sticky rubber" problem that catches up with nearly all F100s, F5s, and D1-3 cameras.
Honestly, right now, with nearly every professional Nikon body extremely cheap, the market is probably a bit saturated for the less popular options. You'll still pay dearly for an F6, FM-3A, or nice FM2n though!