I'm currently in a testing game, and I've found that the AI is fond of using a few Medium ship designs which are notably lacking in the move-speed stat.
Though the Yor faction I've found making this mistake have stronger fleets than the oposing force, they are being outmaneuvered, with starbases, planetary guardian ships, and troop transports being picked off by their faster enemies.
Please not it is turn 352. The Yor in question do have Ion drives available, but are building these ship designs which don't incorporate them.
I took a look through the blueprints, and the issue is caused by the CorvetteL blueprint (see bottom left of screenshot) having its InterStellarDrive component too late in the blueprint, given how little priority the AI gives to miniaturization. It basically starts with a beam RoF component and then loads up on 6+ beams. This gives the design a very high threat/cost and threat/mass ratio, which I believe is why the AI favours it.
Another design they favour is the Paladin, which also will quite simply not ever get an InterStellarDrive to raise it from its base speed with how its blueprint is configured.
Meta problem: Most people will not be experiencing this issue, or at least not as severely, because currently the stock AI cannot build -L variant ships due to a typo/error in ComponentClassDefs rendering them un-accessible in blueprints. I mod-fixed that issue myself, and the result is the AI favouring these ships. The Paladins though are available to both players and AI just fine.
If the ShipClass, Blueprint, and ComponentType issues are fixed, this bug will appear
A save of the above game is here: https://dl.dropboxusercontent.com/u/45479330/GC3/Soak-test%20AI%20at%20war2.GC3Sav
Please do forgive my constant hammering on Blueprint issues, problems in how the AI designs ships just cause all kind of headaches in all facets of the game.