Its not things like Solo modes and the like that cause the problem for me . The number 1 issue (though not the only one) is the weapons (and the issues that have arisen because of that). They do not fall on the same scale as the ones in the other games. The standard Marine bolter does 2d10+5... more than a heavy bolter. Firstly this is daft (not just because I don't actually like the whole concept of the "Astartes Bolter", but that is another issue entirely), and secondly this does not match with already established Space Marine bolters in the Dark Heresy line. Now, this has knock on effects elsewhere, such as the damage of other weapons (most obviously the Marine heavy bolter) and the write ups for adversaries. The original ones in the rulebook just didn't cut the mustard because of the daft weapon damages, and since then many creatures have been obviously beefed up in order to present some sort of challenge because of this (the prevalence of huge wound totals being one example, and the number of elites running around with TB of 18+ being another).
As you suggest you could use the Errata weapon damages (which I do when playing Deathwatch, and they are a big improvement), but this causes problems of its own. 1) Due to the fact these stats are "optional" the adversaries had to be built for the original weapon stats as well as the new ones. This means that many creatures that bolters should be able to hurt, but just not that much, are at a level where the only way the new damages can actually do anything is if they roll 10. This is an issue internal to Deathwatch so doesn't necessarily directly affect this discussion. 2) Many of the new weapon stats are very much "gamist" stats. I mean this in the sense that they are not designed with representing the effects of the weapons in the game system in mind, but to balance them (this is not unique to Deathwatch. Dark Heresy plasma weapons are similar, though consequently make them rubbish). Space Marine boltguns are capable of automatic fire, but with the errataed weapon stats they don't. Game balance wise this is understandable (it stops normal bolters slaughtering Hordes all on their own), but if you then put them alongside most Dark Heresy weapons they don't represent their capabilities very well.
These are not issues if you stay within Deathwatch, but trying to port across and they are.
Ok, I will admit the Parry issue is easy to solve, at least at the basic levels (just presume all careers start with Parry +0 and be done with it). It takes a little thought to think about when they should be able to get it on their career progression and the cost, but it wouldn't be too difficult. I do think the combining skills issue is more important though.
Career progression: The various lines are not balanced against each other. A Dark Heresy character of equal xp to a Rogue Trader character will almost always be superior. Ok, at the level RT characters start out they may out perform Dark Heresy characters in being jack-of-all-trades (due to higher stats), but Dark Heresy characters will almost certainly outperform them in their specialisation, and eventually they catch up at being jack-of-all trades as well.