The free-flow issue is a moot(sp) point because you can simply switch to another second stage without losing hardly any gas at all. Most of my dives are stage dives, which gives me access to several 2nd stages. Changing a 2nd underwater isn't very difficult, even in no vis situations.
Long hose comes into play when diving with others. I switch very often, and always maintain more air on the long hose than the short, but independents are mainly for soloing anyway. You don't need a long hose for yourself. It does take practice to make donating second nature, but what else are you gonna do on long hangs?
As for keeping up with which reg and what guage, color coded zip ties work for me.
Independents are more work and less practical for some people, but under certain conditions I believe they actually increase safety. If not, I wouldn't dive independents at all.