That is really the only problem I have with the P25 systems. The CODEC technology seems ancient. They need the high quality voice CODECs used in modern VOIP and cell phones rather that 15-20 year old CODECs they're using now.
It's not just the codec, it's the available channel bandwidth that comes into play. Narrowband LMR systems need to compress everything into 12.5 kHz RF channels widths, 6.25 kHz RF channel widths, and now even 3.125 kHz channel widths. Cellphone systems don't have the same restrictions.
And consumer cell phones are designed to work in relative high level RF areas (the systems are designed to "saturate" the area with fairly high RF levels) so the receivers don't need to be super sensitive, unlike LMR systems wherein the levels can very often be just above the noise floor.
Plus, the emphasis in digital LMR audio is in voice readability under extreme conditions - lots of noise and fading, etc. You want the words understood as a last resort at the expense of fidelity.
That said, P25, and most other modern LMR digital modes, use AMBE vocoders. IMBE was the precurser and the original P25 vocoder. AMBE is backward compatible with IMBE. Frankly, it amazes me how well they work with voice in such narrow bandwidths.
I still think you may be hearing noty yet fully configured or "fine tuned" system issues (including the one brought up that you may be hearing hybrid patched analog-to-digital and/or vice-versa audio).
I am pretty picky about digital audio in LMR cases and remember the early IMBE stuff and how "bad" it sounded to my analog FM trained ears. But I have noticed how much better it has gotten since, even just using consumer scanner receivers. The DSP code keeps getting improved as does the hardware.
The system I monitor in San Diego County is a mix of P1 and P2 on a fully digital countywide trunked system. Using the P25RX, as you do, I am frankly little short of stunned at how well it now sounds! As close to analog +/- 5kHz deviation (now called "wideband") FM as I have ever heard it sound! With the possible exception of the school bus folks who, I believe, probably get the lower tier equipment (though they are obviously P2 sooo...??) and seem to be the least radio-savvy in terms of how to speak when using the radio (I swear, they seem to be ALWAYS yelling including even the dispatchers!).
Anyway, point is, I think given some more time for adjustment, build out, testing, re-adjustment, etc., your area system may drastically improve. Time will tell.
Also, on the P25RX, don't forget you can play with the channel band filters a bit - that may allow you to improve things a little.
-Mike