I suppose it all depends on what your priorities are, as the OP says.
The creation of emulators for classic computers and consoles is one of the best things that ever happened to the PC, and every PC that I've built for myself over the last fifteen years has had some sort of emulator installed on it. They're especially useful to me as development tools, particularly for unit testing of new software for classic systems, because they're far more efficient than burning an EPROM or uploading code to the original machine to test every tweak. If the emulator has a built-in monitor or debugger, so much the better.
As for playing games, it's difficult to make a blanket statement about whether I prefer emulation to "the real thing", because it all depends on the system being emulated and how I'm interested in using it. For the systems I use the most and am most familiar with, I generally prefer the original hardware. I enjoy playing the games on the original systems
(and a genuine CRT television, if that's what they were designed for) as a total, integrated experience: it's the only way to play the games as the developers and designers intended them to be played. But emulation is sometimes the only viable option for me in the case of exceedingly rare systems, for platforms that would be impractical for me to own (such as arcade cabinets), or for systems that only have a handful of games that I'm interested in playing. I'm generally content using emulators in these cases. Playing NES and Genesis games on the original systems, for example, doesn't add enough to the experience to make the systems themselves worth owning for me, mainly because they're both popular systems for which there are many well-polished emulators available, so the few games I like on those systems are usually played in an emulator.
Having said all that, for my "core" systems, I still find emulators to be inferior to the original hardware for reasons that have nothing to do with the emulation authors or the quality of their work. First of all, flat plastic LCD displays are just a poor substitute for phosphors shining through a glass tube. The increased clarity of LCD make the graphics look too blocky, you lose many of the effects (such as phosphor bleed) that the games were designed to take advantage of, and the reproduction of the original colors and brightness levels never seems to be quite right. I'm aware of the various options for "simulating" some of these effects, such as the garish "scanline effect" offered by many emulators, but it's still not the same. LCD monitors also look like ass if they're not used at their native resolution, whereas CRT monitors can handle lower or "non-standard" resolutions with ease. Sound is another issue for me: I have a hard time explaining exactly why, but the sounds and music from an emulator often seem "colder" or more "hollow" to my ears compared to those produced by the original hardware.
All of this assumes that the emulators themselves are 100% accurate, and the ones for the more popular systems are probably approaching that now. But many times, that's not the case: there are certain niche platforms that only have one incomplete and often unsupported emulator, and for some systems, there simply isn't a viable emulator available at all. The most notable example of the latter that I can think of is the Atari Jaguar, but given the bizarre attitudes of that "community," I suppose it's because emulation authors are simply afraid of being burned at the stake.
There's also the question of how to adequately simulate the original controllers. For systems that used gamepads, like the aforementioned NES and Genesis, I generally don't have a problem mapping the original controls onto modern gamepads and using those instead; I usually prefer them to the originals anyway. For other systems, there are USB adapters available for the original controllers, although they sometimes introduce noticeable amounts of lag. That seems to be true of the paddle adapters I've read about, which is especially problematic considering how timing-sensitive many paddle games were. But there are certain weird exceptions that are much more difficult to emulate. Imagine an Intellivision with two 16-direction hand controllers--both with their own 12-button keypads and side buttons--connected to an ECS Computer Adaptor with a Computer Keyboard or Music Synthesizer plugged into it. You'll never find a satisfactory way to simulate all that on a modern system.
I suppose I prefer using the original hardware for the same kinds of reasons that many golden-eared audiophiles
still prefer listening to their music from LP records instead of Compact Discs. If you look into the kinds of arguments they offer in support of their position, and at the kinds of subtle differences which they can notice but that the less-discerning public might easily miss, there are certain similarities to what I've written about here. Again, it all depends on the level of enjoyment you're looking for. As they say, de gustibus non est disputandem.