I don't feel like getting into the whole big thalmor debates again right now, so I'll just adress the OP's question about what I'd do if I commanded either side's army:
Thalmor: I'd never've invaded Cyrodiil. Instead, I'd've purged the AD of the blades, then proposed the following deal to the Emperor: allow Thalmor Agents to travel openly through your lands, and we'll destroy the DB, Daedra cults, and other padomic groups. In exchange, we'd end the Skooma trade to Cyrodiil. If he accepted, we'd do as we said (which they proved themselves capable of in the great war), greatly reducing human access to Daedric Artifacts, unleashing hordes of strung-out junkies upon Leyawiin, and get rid of one of the great outlets of human psychopathy. We'd try to use the excess sugar to mess with either the Sload, or the Maormer. Regardless of whether or not the deal was taken, we'd focus first on invading Thras and Padonyea. At the same time, we'd try to establish relations with the Hist, Ka'Po'Tun, and the legendary surviving dragons (I'm talking about the ones who were there even before the events of Skyrim). Thras and Padonyea are far more obtainable goals, and make far better use of Altmeri seapower, than "the whole of Tamriel", + diplomacy rocks, + the spiritual battle against Padomics is most important.
Empire: I'd've sent a ghost fleet (lots of ships with very few men) sailing for Alinor, and had all my island holdings pretend to be better manned than they were (have more blokes on the wall than is normal). That'd hopefully freak the Altmer right the eff out and mess with their tempo. Besides that, I'd also try to leverage Titus Mede II's obvious daedric ties (he wielded Goldenbrand) for greater influence. That's really all that a commander could do. The Empire's errors were mostly due to the nature of surprise attacks. No genius plans I could hatch would really have much of a chance of getting implemented with all our forces scattered.
I suspect that man-for-man in a straight fight, Goblin hordes (who fear the lash) are a lot less effective than Imperial legionnaires (with the love of Empire Actual in their hearts).
Now, this is really rather silly to think about, but from what we've seen of imperial tactics & outfitting, the goblins should actually have a huge physical (if not morale) advantage over the humans. Shin & lower thigh protection is highly de-emphasized by imperial armor, while they favor stricking weapons of lengths insufficient to be effective versus a near-ground target. It's essentially a classic case of the left-handed advantage: both the tall men and the short goblins are trained to fight tall foes, because tall foes are more common. This renders the tall men's training slightly inapplicable, but leaves the short goblin's training wholly relevant. Having the three shortest armed forces (goblin, bosmer, and four-legged Khajiit) on their side really is a very strong advantage.