Jeremy,
No problem at all... I've been pretty disappointed with the audio forums on this site (which I guess is understandable considering this is mostly a performance / repair oriented site), so I'll try to contribute wherever I can...
Simply put, there is only so much you can do with a 4" speaker... No matter how "good" the speaker is, it will never be able to produce an acceptable portion of the audible frequency range... While you can compensate for some of that lost low end using a subwoofer, you are still losing a substantial portion of midbass (as most subwoofers aren't really efficient over 80hz, and most 4" speakers aren't really efficient below 120hz, so you're losing that entire 40hz spectrum)... Most 6.5" speakers can comfortably be crossed-over at 80hz, so while there may be an awkward transition from sub to midbass (different issue for a different topic), at least you have the entire range.
Toyota obviously threw the sound system in these cars (and several other models of theirs) as an afterthought... In all fairness, it's not just Toyota, it's many manufacturers... They simply put whatever size speaker would fit, wherever it would fit (fortunately these manufacturers have become more wise to the fact that audio is becomming an important factor, and they generally have better layouts in newer vehicles)... The rear speakers should NEVER be larger than the front... The fronts should always be the same, if not larger than the rears... Even people who aren't audio purists generally prefer to be immersed in the sound, with a slightly forward sound stage (purists actually prefer the full front sound stage with minimal rear fill)... Fortunately our Supras at least have the front speakers in the doors, which require very little modification in order to fit the speaker sizes we really want (even without getting a hold of the '91+ speaker pods it's simple to fabricate MDF spacers to fit 6.5" speakers in the factory locations), and you don't have to cut holes in the trim (so the interior of the car appears stock). I would recommend trimming the holes where the 4" speakers used to fire through in order to get the most out of the larger speakers, but this isn't necessary.
For speakers to check out... I'd at least take a look at Boston Acoustics SL series, Alpine Type S and Type R series and Eclipse Point Source series (of these I like the Alpine Rs and the Boston SLs the best). The reasons I'm recommending these speakers are that #1 they offer EXCELLENT sound quality, especially for the money spent on them, #2 they are easy to find, #3 they can be had for very reasonable prices if you look in the right places, and #4 they will all sound very good powered straight off an aftermarket headunit, however they will all sound much better if powered by an external amp (so basically, you will be very pleased powering them straight off the head, however they give you plenty of room for upgrading). There are plenty of other speakers out there as well, but I've been impressed by each of the speakers I mentioned for different reasons...
As far as subs go... I'd go for a single or pair of 10" subs to best suit your rock/metal needs. A 10" sub will generally be more responsive than larger cones, which is a huge benefit for guitar and percussion. They won't offer as much low end as larger subs, which is a mild trade off for the added responsiveness, however that wont really come into play as much unless you listen to industrial, electronica or other types of music that are more heavily dependent on the lower ends of the spectrum. On the other end, a 10" does offer deeper bass, and is nearly as accurate as an 8" sub, and will offer more low end "kick". A couple added perks of going with a 10" over a larger sub are the facts that they usually take up less space, require less power and weigh a bit less than comparable 12"+ subs ;-). I'd check out JL W3v2s, W3v3s and Alpine Type Rs... All three subs are VERY impressive, and can be had for a reasonable amount. Also, they don't require a lot of power to drive efficiently, however they will take (and love) whatever you throw at them. Go for a ported or vented box (not a bandpass, but a box) to best suit your music. Just make sure it's built / tuned to the specifications of whichever sub you wind up with.
I'm, personally, a huge fan of capacitors... There is a lot of debate as to whether or not capacitors really make a difference, however this is heavily based on the misunderstanding of what capacitors are really intended for... Capacitors are NOT a replacement for upgraded batteries or alternators, they are simply a buffer to your vehicles electrical system. The reduction in light dimming and such are positive side effects, however adding a cap is not the cure for alternator whine, dimming lights, clipping, amplifier cut-out, etc... The first thing you should do if you experience light dimming or other power related issues is upgrade your battery... I'm not saying you should go all out with an Optima or an Odyssey Dry-cell... a $60 battery with a larger power reserve and more Cold Cranking Amps should be all it takes, especially if your current battery has a bit of age on it (assuming you aren't pushing kilowatts). Now, with all that said, a capacitor will DEFINITELY benefit your sound system... It will usually extend your battery life, alternator life, prevent power surges and reduce the effects of temporary power dips. It will protect your amps AND your electrical system... I'm not sure how much power you are looking to run, but most people recommend going for 1 Farad per 1000 Watts (RMS) you are running... With the cost of capacitors now-a-days, I'd say double that (there's never any harm in extra capacity)... I ran a 5 Farad cap while running around 1800 Watts RMS...
If you decide not to go for a cap up front, I'd definitely leave room for expansion... The easiest way to do this is to run your power from your battery to the rear seats and split it with a THREE-way distributor block to both of your amps (assuming you're using 2 amps)... That way you have the third output when you decide to add the cap. I'd use a three-way distributor even if you're only running one amp for the same reason (you can add a second amp and a cap later on without rewiring). Just makes life a bit easier ;-).
Anyhow, sorry for the long post... I hope I've helped at least a bit. Feel free to ask any other questions you may have and I'll get to them when possible.
Take care,
-James
