If you're interested in, say, endurance-related MMA training, it's actually possible to accomplish both in the same cycle. Now, if you were really out of shape or were interested in surviving a 15-minute sparring match, then it would be better allot one entire cycle for endurance-related conditioning. And then, in the next cycle, mantain that conditioning while working on increasing strength and size. It also happens that, provided you eat big, the former could facilitate sarcomere hypertrophy for the latter by increasing protein turnover rates and bodyfat utilization.
Really depends on context. Building basic aerobic capacity/cardiovascular endurance to an acceptable level isn't hard in itself. You just throw in cardio sessions into your strength training or HST program. Besides possible RBE issues, that won't cause significant problems with gaining mass provided you adjust your caloric intake. Now, building such so that you're Lance Armstrong or a mid-fielder worthy of Arsenal, well, that's a completely different story. That would be difficult to accomplish while increasing your LBM due to the enormous metabolic resources it would impose on your body.
For less ambitious goals, you could set up your endurance/power cycle like this:
For the first 2-4 weeks, start with some form of localized density training. Density training has been recently hyped up in MMA circles; but in my opinion, a practical application of density training needs to consider neural drive and differentiate between "localized" and "systemic" in deference to that. The localized form would basically be a more general form of lactic acid threshhold training. You would basically target a set of muscles session to session, and apply a DT schedule to single-joint and pulling movements. The domain of muscles would be the major functional muscles of your body -- legs, mid-upper back, abs, arms, forearms. The key that, in this phase, the emphasis is placed on producing extremely high, dehibiliating levels of lactic acid, but methodically and in in short burts. Area to area, rather than as one full body, which in turn lessens the extreme amounts of neural drive and overall energy demands. Also, during this phase, you would add in some kind of cardio to improve aerobic capacity.
For the next 4-6 weeks, you would then switch to a strength cycle or "heavier" HST cycle (i.e. start through 5s or near end of 10s.) You then make the judgement call as to how much you want to further increase your endurance levels. You could judiciously add metabolic stress techniques (15s, drops, pulses, etc.), which would be much less than what you did during the first 2-3 weeks, but still high enough to mantain or improve your energy systems.
If, however, you want to work harder, than you switch up to more systemic density training scheme, performed two or three times a week, in addition to your program. Rather than concentrating on hitting muscle groups, you would introduce more general movements, such as kettleball or rod training, squats, chins, snatch-and-jerk, etc.. Your density sessions would be longer and more taxing energetically, but the localized lactic acid would be significantly less. However, from a visceral respect, it would be easier to endure than your first 2-3 weeks.
The logistical issue would be, during this 2nd phase, would be to balance how much of the systemic density training you would, in comparison with how much strength-related or hypertrophy-related work you do. And, of course, you'll have to eat like a loony to reap the mass-gaining benefits from this.
cheers,
Jules