I've had Wrangler my whole life. I've been an audio nerd my whole life. I run live sound for concerts as a hobby mixing everything from string quartets to punk rock.
BASIC:
Start with ditching the stock speakers and going with 5.25" coaxials all around and a new headunit. The new headunit, regardless of manufacturer or what RMS they claim, will put out about 22W RMS with a typical car speaker 4Ω load and be much better than the stock stereo, mainly for the ability to EQ the speakers. Always use the high-pass (low cut) filter at 100 Hz with a 12 or 18 dB per octave slope.
MEDIUM:
If you're going into the subwoofer realm, that is really where the sound starts to pick up in a Wrangler: there's no mid-bass or bottom end below 100 Hz, even if you throw 6.5" speakers in the rollbar. They're all basically free-air, underdamped, and floppy below 80 Hz or so. Adding polyfill and an aperiodic vent only helps a bit. You will gain very little bass reinforcement from any rollbar or even the front speaker pods—the air pressure simply can't make it out from the restrictive dash. You're just hearing things rattle, at a time delay, which is why things don't sound "tight." Throw a sealed 8" in and your whole system's volume will reduce drastically because you aren't blasting the knob just to feel a feeling.
BEST CASE (so far):
Once you have a sub to handle things below 80-100 Hz or so (which ever cross-over point sounds right to you for the speakers you get), use component speakers up front to get the tweeter on top of the dash, as far back against the windshield as possible. It's no-where near ideal, but if you get the face of the tweeter close to match the distance the front speaker cone is from your ear (the voice coil, more accurately), you'll have very little time-alignment issues from the front crossover from tweeter to woofer. I don't hear any in mine.
Anything above 2500 Hz or so isn't heard very well until this is done—you're only hearing the second and third round of reflections until you do. Coaxials up front are aimed down at the seat ... through a thick plastic slotted grill ... almost 6–8" before the grill even starts ... most of the sound is going down or reflecting off the dash and firewall and up to you. Even if you cut the speaker grill out, you're listening to the woofer/tweeter at more than 45º off-axis. Unless you have 48 bands of EQ, there's really no correcting physics.
I've thrown high-end speakers thinking this will get me bass and clarity ... well, not unless you throw a regular size amp at them, and only if you get them into tuned enclosures. I run Hertz component speakers, but I've heard a full set of amped Rainbow speakers in a TJ and they aren't much better. You're just hearing rattling and resonances from anything below 125 hz unless through a subwoofer in a proper box.
The only way to get things sounding "right" in a Wrangler, not just loud, is adding time delay to the rear speakers. The rollbar speakers are literally 6" from my ears ... the front speakers are about 2–3 ft away. Psychoacoustics is everything: this causes your mind's ear to hear the music like it's coming from the REAR. The sound from the front speakers arrives in 2.7 ms, but you hear your rollbar speakers only 0.44 ms after the same tone is played ... you hear your rear speakers in almost 1/6 the time that it takes for your fronts to get to your head. Add a 2.0–2.5 ms delay to the rear speakers (you'll hear it when it sounds right) and be surprised when the volume knob gets turned way down ... you'll realize how much you've been turning up your speaker to hear them better, when all you're doing it making the interference louder.
Especially at sensitive frequencies (human speech is ~300–4000 Hz) humans can perceive a 0.5 ms delay easily ... this is havoc on our psychoacoustics. To pan an instrument from left to right on stage, you don't pan them to the right: you add delay to them on the left stereo output. This sounds, to your brain, like the sound is shifting to the right. Same thing happens when you delay the rear speakers in a Wrangler: they're no longer fighting the fronts, but reinforcing them and as time-aligned as your pedantic self would want.
I also added a "BBC dip" from 3.5–5.5 kHz and a high shelf from 5 kHz to 20 kHz ... with the tweeters on the dash, I actually have to EQ them down so things don't sound too bright and fatiguing. No more high loss at speed with no top or doors now though: you can hear it all.
MOST IMPORTANT THING for okay sound in a Wrangler: high pass filter (low cut). If you don't use a subwoofer, ENSURE the headunit you get has at least five bands of EQ and a high pass filter for all speakers. This cuts the bass being sent to the speaker (no sub, set it to 100 Hz at a 12 or 18 dB slope) and gets rid of all the low crap the speaker can't reproduce effectively, overall cleaning up the sound A TON. Don't worry, you'll still hear the bass guitar, just not the fundamental: you'll hear the harmonics which I'd prefer over a floppy, distorted bass tone.
Alright I've said what I need to! Good luck!