The "glory days of indies" might have returned if MNTV had never existed in the first place, and then the spectrum auction might not be as big a thing as it is. But MNT, the reality facing indies today, and the spectrum auction itself are all symptoms of a larger malaise hovering over broadcasting as a whole, a structural problem that makes it utterly inviable to enter broadcasting if you aren't already in because of deep disadvantages in acquiring programming and attracting an audience compared to cable.
Worth noting that nearly every market in the top 15 or so has at least one traditional independent, and beyond the top 60-70 at least one of the CW or MyNet is on a digital subchannel (why there are subchannels whose sole purpose is to show ten hours a week of a "programming service" showing nothing but programming probably available elsewhere continues to utterly baffle me), so MyNet is really serving the needs of a rather small bracket of stations by filling a mere 10 hours a week. Admittedly it's the most difficult ten hours to make anything of, but a number of stations that are sisters to Big Four stations (or even not) have success running news in primetime, and when Fox's own MyNet station here in Los Angeles is punting MyNet programming to nighttime, it's clear that filling the time is not the only reason for MyNet's continued existence. They don't want any broadcast stations getting uppity and signing up for anything that might provide actual competition for any of their businesses they actually care about.
In retrospect, the best thing currently-MyNet and independent stations could have done would have been to make an investment into major-league and -conference sports programming, but it's not clear that ever would have been possible without major changes to the rules governing broadcast considering how much major-pro-team programming had already moved to regional sports networks by that point, the launch of the Big Ten Network the year after MyNet's launch making conference-specific cable networks the next big thing all the major conferences wanted to jump on board of, and ESPN's acquisition of the Bowl Championship Series the year after that putting the writing on the wall for broadcast's viability in its own right. Cable's ability to take advantage of the dual revenue stream of advertising and subscription revenue made it unbeatable when it came to acquiring sports rights (or any other programming) with broadcast having only the PR value of marginally wider distribution left, and broadcast's response was to chase retransmission consent revenue that only made them dependent on cable companies for distribution and led them to disdain their own nominal medium, and cord-cutting is acting too slowly at undermining that dual revenue stream for broadcast to benefit from it, certainly in time to stop the auction from taking away a bunch of otherwise-valuable stations.
But sports is so valuable precisely because live programming is the sole purpose of linear television anymore, its one advantage over time-shifting and Internet-based viewing, broadcasting is theoretically a more important vector for linear television than cable because of its theoretical ability to reach mobile devices directly (though it hasn't exactly been able to get that straight), and rights to local professional and college teams are precisely the sort of thing that serves the purpose of localism that broadcasting is supposed to serve but hasn't outside news for decades. If broadcasters weren't a bunch of cheapskates but actually knew what they were doing and were actually able to do it, the stations most able to do it in the largest markets weren't owned by the very entities they'd be trying to go against, and if all involved parties weren't more concerned about preserving their retrans revenue than changing the circumstances that make it necessary, the incentive auction wouldn't even be a problem and no one would even consider broadcasting a relic of a bygone age.
It all comes down to the bad rules governing broadcasting; they continue to be rooted in principles that don't reflect modern market realities and so make it that no one in their right mind would go into broadcasting that wasn't already in, the duopoly rules are completely backwards and allow duopolies in the markets where they're most harmful and forbid them in the places where they're most beneficial, no one has bothered to think that maybe changing the rules BEFORE holding the auction might impact the outcome of it (not even bothering to enact rules based on size of spectrum, thus allowing duopolies to consolidate into a single license while smaller stations channel-share to achieve the exact same result, potentially allowing some companies to control FOUR TIMES the amount of spectrum as others despite being officially discouraged), or if they have they've decided to hold off until afterwards because they see broadcasters as a cash machine and an obstacle in the way of wireless companies rather than a way to potentially curb the wireless companies' voracious spectrum appetite they'd rather feed instead, they've dilly-dallied on doing anything about the "people paying for stuff they don't watch" problem because Disney spends millions keeping ESPN's business model intact at all costs and cable companies are ultimately going to suffer most from it, I could go on and on but this rant is long enough already.