Part of the problem with the old transport system, if I remember correctly from the devs, is that it's incredibly complicated for the AI to use and plan around. It requires quite some planning ahead. It wants these units to cross the water so it needs a transport, that transport needs to be at that location at that the same turn the stack is there, but things can happen in between like the transport getting attacked and so on. It's all not very complicated for humans, but for AIs it was apparently very difficult to actually get right. Indeed, in Age of Wonders 1 the AI never built boats and never used transports at all. The Flood spell from the water sphere was horribly overpowered against the AI as it'd completely immobilise any non-flying non-floating non-swimming units they had. I don't think the AI used any transports in Shadow Magic either. In the end they ended up with the embarking system for Age of Wonders 3 because it was far simpler for the AI to use.
