You did not say exactly what improvements you want to make, what your budget is, nor if you are looking for a stealth install.
First I'd recommend that you look at what some other owners have done and see what you like. The MR2 Owners Club Forum
would be one place to start. Many times you will find unbiased reviews of specific gear. There are installs documented with photos, and detailed step-by-step procedures. Generic car audio forums are also good. For comparing equipment and pricing, you simply cannot beat Crutchfield.
The prices at Crutchfield are generally lower than you will find at your local audio dealer, but somewhat higher than other online stores. But they are excellent for doing research and if you do buy from them, you will find that the extra dollars paid buys you the absolute best service available.
If you're looking just to add an amp and a sub or two, and want a custom look instead of a "big ugly box", you might want to check out Concept Enclosures
. He constructs custom boxes to fit specific places. Sort of like the JL Audio stealth box, or MTX Thunderforms, but less expensive. He has a design for the MR2.
And if you just want to change out your factory speakers, while you are browsing the Crutchfield site, check out the Focal speakers. The Utopia Be NO. 7 is simply the best 6.5 " 3-way component automotive speaker system in the world period. But if your budget won't stretch for the Focal's, consider the Alpine SPS-600C component system. They sound amazing.
Hope this helps.