Been looking at the RT document a bit lately, and there are a few issues. Firstly, costs. Some ships are just too expensive. The armed cargo transport is not worth 20 pts. Sure, if you're playing some sort of convoy scenario a fast clipper could be useful, but it's probably still not worth 20 pts, since it's only half a transport (meaning you're paying 40 pts per full transport to upgrade their speed). This should come down to 15 pts at most. Repair Tenders should cost no more than the any other heavy transport, being self balancing. Super-heavy Transports should cost no more than +20 pts. You gain no firepower/range, have to use a large base, have a worse turning circle, and only gain 4 hits and 1 transport capacity. Comparing 2 Super-heavy transports to 3 heavy transports the heavy transports come out ahead, so +50 pts for those extra 4 hits really is insane. Xenos vessels are also overpriced. They're essentially slow, expensive Idolators. Their targeting system (one of the best upgrade choices) is slightly better than the Idolators and some may think it's worth 5 pts more than an Idolator (despite the loss of speed) but then again, the Idolator itself is overpriced.
While we're at it, even though they're from different sources, the Q-ship overpriced by at least 10 pts and the Iconoclast should be 25 pts. Oh, and I'm also a little dubious about the 15 pt premium on lance or long range ships. It means that the only full cruiser you buy at cost is the Tyrant, which has only 4WB@45cm rather than the 6WB@45cm of the base Rogue Trader (so you gain 2 torps in return for the loss of range).
The upgrade rules also really need a rewrite. Firstly, the "Rogue Trader Cruiser" needs to be renamed. If a Rogue Trader can take a Carnage and this ship counts as a Rogue Trader cruiser (as a cruiser used by Rogue Traders rather than an allied cruiser) then it becomes unclear what is meant by the term "Rogue Trader cruiser". Does this mean the specific class of ship or any non-allied cruiser? For example it says that at least half of the cruisers in a RT fleet must be a RT cruiser or Endeavour. In this context I'm fairly sure that the "RT cruiser" bit refers to the specific class. However, I'm not so sure of this definition when it comes to purchasing a crew skill. If we're being consistent then it would mean that a Rogue Trader Lunar, say, couldn't purchase a crew skill. That seems weird.
The Xenotech systems needs to be reworded. The way it's worded now you may give any RT vessel a Xenotech system. So if you were to take a squadron of 6 escorts you could give 1 of them Improved Sensors and 1 of them an extra shield (on point) and leave the rest with nothing. I'm not sure this is the intent. For example, Auxiliary vessels in a RT escort squadrons can "benefit" from Xenotech if there are at least 3 RT escorts in the squadron. This implies that the Xenotech upgrade is a squadron wide upgrade, such that they must all take the one. Secondly, Heavy Transports can take a Xenotech system, but it isn't known whether you can select the upgrade. As it happens you should be allowed to select the Xenotech upgrade at all times, but some should just cost more. For example, for a cruiser the upgrades could cost +10 pts with another +5 pts for the shield or targeting system. For escorts it'd be 5/10.
The fleet composition rules are also pretty terrible in general. For example, in the "RT in BFG" section, what constitutes a "cargo ship"? Is an escort carrier a cargo ship? It looks like one, but it doesn't count as a transport. Similarly Q-ships aren't actually transports, but they're specifically designed to operate in transport squadrons. Armed Freighters do count as transports, but why should they be allowed and the other 2 not? Heavy transports are transports but they also appear in the capital ship section, which suggests that you can only have 1 (or 1 per 750 pts in Demiurg, Tau or Imperial), not any number. RT armed cargo ships are transports, can they be taken in unlimited numbers, with other transport ships? Speaking of which, they give +1 to RO tests because of surplus torps, so when used in a squadron with escort carriers (see pirate list) do they still give +1 to RO tests?
Overall the terminology needs tightening up, the costs need rejigging and the composition restrictions need to be looked at hard.