The cargo ability allowing SYS on transport hulls is intentional. There are some other components that also benefit from that (supply storage, for example). This creates an interesting design choice, in addition to introducing SYS before cruiser-sized warships. That is, players have a choice between less capable (slower, bad combat ability) support ships at reduced cost, or expensive Versions with the same speed and ability levels as warships (minus the tonnage for the support components).
Unfortunately, the AI seems to have no ability to use SYS to any advantage, even if they can be made to build them.
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As for JLS's questions about effects of the proposed computers change on existing games... it could be made so the AI would phase out the MC's. Human players wanting them would then need to research the new tech area to get them. It's not a very elegant solution, but it seems better to me than the alternatives I can think of at the moment.
PTF's suggestion about reducing subverter accuracy is another way to possibly help.
Perhaps there should be a set of optional patches which players can choose from to get the changes they want to deal with it. Yeech.
PvK