I finally found the time to put together my thoughts on this one.
I'll agree with the others on the tension issue. Even before I read your comments, I realized this was supposed to set up how well the Trodoons were doing, so it becomes difficult to establish tension through that. One way might be to send other fleets off without Darkclaw, so we have to wait for the results, but that doesn't seem in the character of this story. Another might be to play up the possibility of other ships leaving; if Darkclaw is truly concerned about word getting out, that should be the primary focus of his attention throughout the battles.
Along those lines, what's to stop any old ship from showing up, realizing somethings going on, and turning tail? Something like that is hard to prevent... so I'd have Darkclaw worrying over it, and coming up with contingency plans, or something like that.
At the beginning, Darkclaw has learned "little that would be of tactical use". I doubt any library would have that little of information, especially for a race that knows little of the rest of the universe at all. What I would believe, however, is that he can't recognize the information that would be tactically valuable, and that which won't, so he's got to go through it all and try to remember it all. There should also be a lot of strategic information, loads and loads, which probably couldn't be completely covered in three years, let alone months.
Darkclaw thinks that the Alliance navy won't be able to resupply ships as quickly as his station, even though they have all those shipyards. I realize that Selixan station is large and cool, but first of all, one station, no matter how big, wouldn't be able to keep up with a variety of other shipyards, many of which are probably stations or planet-based (that is, have more or less equivalent resourced and manpower). Second of all, if it can crank out ships that quickly (and crew, but clones cover that aspect), Darkclaw should probably wait a bit longer and build up a larger force. Having them in hand is more valuable than replacements, generally speaking, although you'll want replacements eventually as well.
Darkclaw also thinks that they'll change the destiny of the galaxy in a few short hours. I wasn't thinking the planets were quite that close together, even through hyperspace. If that is the case, I would expect traffic between most planets nearly every day, so it would become quite obvious if some planets suddenly dropped off communications.
A passing reference to the high command being non-cloned made me wonder if the cloned troops have any special powers, either.
Praetor Keeneye asks about the Reathan system in the middle of the briefing. However, Darkclaw started the briefing by saying they were going to take Reathan, so that seemed odd to me.
After developing the detailed plans for the other two systems, Darkclaw just waves his hands and says, in effect, Reathan isn't worth even planning? No military commander would ever do that, especially not one that developed such specific plans for the other systems. At the very least, they'd say their plan is to come in close to the planet and bombard it.
Also about the planning, I don't know if we need the detailed plans given to us, plus all the battles. One or the other should be fine, with a summary or reference to the rest.
When they are ready to start, Darkclaw orders the crew to battle stations. Even if it only takes a couple hours through hyperspace to get there, that's too early. At most, they need to be in stations fifteen minutes early (maybe a bit more, if they have checklists to go through), so the call to stations should be 30 minutes or so before arrival. And if your hyperspace travel is such that you can get between systems in a half-hour or less, that implies it's a morning's jaunt to go visit someone (or bring in food, medical supplies, what-have-you), and I'd expect an almost continuous stream of people traveling. Heck, you could almost live on one world and work on another if that's the case (except perhaps for the power required for the ship to cover hyperspace).
The battles seemed a little drawn out, but I think that's because there was so much in a row. A short break to another viewpoint somewhere in there might be nice.
When Darkclaw was watching through Shadowpath's visor (or whatever), Darkclaw mentions seeing from the point of view of a shadow on the floor. Whatever the Trodoon abilities are, I was surprised that the technology seems to work with an effect like that.
Darkclaw with the President: I assume the energy sword was a regular weapon, and not the reason for Darkclaw's name? You set up the beginning with Blackspike's spikes not being as black as Darkclaw's claw, so I was half-expecting to see the claw come out. Also related to this, why did Darkclaw even have to go down to the planet? He could have communicated through a viewscreen if he needed to be personally involved, but he basically wastes time in a shuttle going down and coming back, plus finding where they are, all so he can just behead a guy and get the next one to cooperate? That's why moderately-high level henchmen are for, and Blackspine should have been able to handle it no sweat. Even if he needed orders from Darkclaw to do so.
The commander of the opposing fleet in the second battle (Zyan) did not use good tactics at all in his situation. Now, people do make mistakes, but assuming he could see the ships coming at him, and what they were doing, he should have had ships either going full-bore the opposite direction, or have his whole fleet scatter in an attempt to get at least one ship out and away to warn the alliance navy. In fact, you state that they noticed the stealthed ships already; they may think they have the battle in hand, but seeing stealthed ships appear should ring an alarm that says "send information about this to other systems". He really should have had at least a few ships headed out just in case when that happens. (In fact, that could be used to build tension, if Darkclaw shows up to see at least some ships headed away from him.)
By the time we got to the end, I was happy to see an unexpected patrol show up. They'll probably be wiped out, but if they were smart they'd do an immediate U-turn and head for reinforcements.