Running as part of a good 5 day pt program should be conduct 2x a week. One of these 2 days should be for approx 50 min at a pace 75% of the troops can comfortably maintain. The other run session should be of a variable speed based on interval training, hills, running interspersed with other exercise (not circuit tng), and the various types of training runs can be rotated over a months period. The other three periods during the week should include a ruck march (for us who must complete a BFT), a circut tng session and a sports or fun session (swimming, skating, on own, whatever).
Personally I feel martial arts style training can be supplemented into the pt routine. As a start point do a surge of training (day to week long where everyone becomes fam with the skills) and then add into the pt program once or twice a month to maintain skill memory. That way in preparation to an operation or whatever, a small surge of training should bring up the skill level that will hopefully not be required. I personally feel though if you personally want to maintain your martial arts ability to a fighting level, you really should do it at your local club.
To answer the original question...
Running is the basic excises in order to maintain cardio fitness. It is simple, cheap, and with enough practice anyone can do it sufficiently well to enjoy it. The military tends to ruin it by making it unenjoyable by enforcing group cohesiveness. Good, innovated leaders can find ways to make the old run a bit more exciting and by emphasising individual effort (put an effort in good, if you don't bad*...as a runner I can tell) hopefully encourage improvement to all levels of fitness in your group.
So if you think running is bad, why do so many people do it as a hobby and as a means to maintain a healthy lifestyle?
The answers lie there.
*note-as a det comd in Fd Amb I said that if you could not keep up, thats fine but do not stop running. I put a person on verbal warning for not putting enough effort forth in their pt. The troops heard this, and we didn't have a problem after that. Oh yes, and now a couple years later, that person now runs on their own.