Valid points, but as someone pointed out earlier, with the eventual phasing out of TACANs and the increased reliance on GPS, we are going to look awfully stupid if we do not develop systems for the future.
"Because we've always done it that way" is the absolute WORST reason to do anything - it does nothing but stifle innovation and improvement. FAA-certified GPS, civilian ILS, and RVSM compatibility would go a long way to better integrating military aircraft into a CONUS flying environment. In new "5th gen" aircraft such as the F-22 and F-35 it is ridiculous if such technology isn't integrated.
We can hem and haw all we want about the tactical aspects, which is obviously a primary and huge concern, but we do spend the majority of our time flying in/around civilian airspace and should make an effort to integrate into it when it doesn't compromise the mission capabilities.
I'm not so foolish as to believe it isn't because of something other than $ that it isn't the case, but when we pour millions into projects like the LCS, San Antonio-class LPDs that can't even sail, or the abortion that is the AAAV, it gets hard to swallow that line of reasoning.