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just build a custom small box about the size of the stock one and put a quality 8" sub maybe? honestly anything in the higher end aftermarket will be better than the stock sub.
I am having the same problem with my speakers. Just bought some high quality component speakers and now I'm shopping for an amp. the speakers are 90w RMS and the tweeter is 50w RMS and if that deck only pushes 15W RMS per Chanel I will only be powering those speakers at about 10%.