From what I've seen in the dev streams, the NOD gunship appears to be rather underwhelming. First, I'll talk about my understanding of why it may feel underwhelming/out-of-place, and then talk about what I think could be a possible replacement.
It's a large, aerial unit, and can be hit from just about anywhere - it has to hug either the skybox or the ground in order to survive. In order to be comparable to the mammoth, it also needs to have a pretty absurd hp pool for an aerial unit, and I imagine it's damage output must be quite difficult to balance as well - enough to be a big threat, but not enough to be OP when combined with its vantage point and speed. By comparison, line-of-sight is incredibly important for both the defensiveness, and restricting the offensive capacity of, the MKII,
The gunship is also something that's never appeared in any of the games afaik, and I'm not sure it really fits with NOD's general style - GDI is the one with overwhelming resources and firepower, NOD generally prefers advanced tech and guerilla tactics, so even the idea of an 'epic unit' of that type seems a bit off for NOD at this stage (obviously CABAL has his giant robot, and NOD gets their Avatars in TW but other than that it's not really their thing).
My opinion is that, essentially, NOD should not try to compete with GDI using a like-for-like epic unit - asymmetry between NOD and GDI is one of the best things about C&C and especially Renegade, and as of TS (other than CABAL's giant robot), they just don't have access to anything that compares to the MKII directly. As far as what could possibly fill the void of a MKII for NOD on the battlefield, I think that giving NOD the ability to have up to 4 Cyborg Commandos, who should be seriously powerful, at any given time. I'm not saying that they should be powerful enough to straight up 4v1 a mammoth, but their small size, ability to split up and secure objectives, as well as move across the map more sneakily, potentially using vehicles (although that might be a bit OP - Might be best if they can't pilot), should make them comparable in overall power level.
For GDI troops in the field, coming across even one should be pretty terrifying - the rough power level I envisage for them is that 1 Cyborg vs 2 Titans+pilots should be relatively evenly matched (taking into account the fact that Titans aren't the best vs infantry). Upon hearing that there are Cyborg Commandos on the field, GDI might look to dispatch a squad of wolverines or something to deal with them. They'd also be fantastic at objective defense for NOD - leaving one to defend an outpost while the others take an offensive action along with some stealth tanks. In general, I think it would be a fun way to implement NOD's epic units, and would serve to emphasise to anyone playing, be they an existing C&C fan or not, the very different playstyles and approaches to warfare that GDI and NOD have.
My major worry with using Cyborg Commandos in this way is that if all 4 of them, or even 2 or 3, were to get near GDI's base, they could be uncontestable. Perhaps limiting their building damage, or making them unstealthable, could be sensible. If they're made unstealthable and can't get in vehicles and GDI still can't spot them out before they reach GDI's base, then GDI probably deserves what's coming to them!
