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Doesn't thrawn have better heroes, and thus can make entire fleets more powerful with combat bonuses as a result? Thus thrawn can be more efficient with his power at the cost of a permanent reduction in power if a hero is lost. Palpatine can build and replace more powerful ships, but many are battlecruisers and SSDs that are more vulnerable to bombers. Unless I've misheard the 2.2 playthroughs....
Personally, I think my plan would be to build some awesome stuff before losing Isard, and then using Thrawn as a force multiplier.