Multiple Andalite morphs would have been useful on several occasions, and it definitely would have thrown Visser One off the trail. Only one Andalite ever showing their face was one of the things that tipped her off regarding their identities.
Personally, I'd have them morph more aliens (Leeran, as invasive as it may be, is insanely useful and they're all idiots for not taking advantage of having that morph on their side), and also do rhino more often (seriously, it was awesome every time Jake pulled it out). Maybe some more big cats too. Leopards rocked while they had them, and cheetah should've been used as an interceptor, not a main combat morph.