I think to this point HR has been fantastically written and a total joy to run, but I think HR has a major weakness, which are the rebellion rules. I've only run the suggested trimmed down version of it, because I didn't to play "optimise this excel spreadsheet", but we still felt the massive bonuses the PCs got from the rebellion. I don't think the developers accounted for all the bonuses the PCs would get, so my advice to anyone wanting to run the latter parts of HR: Ramp up your encounters or ignore the Rebellion rules.
I have yet to start HR - not quite halfway through Shattered Star and want to make sure I spend a lot of prep time on HR to give it all the attention it deserves and really make it come alive for my players. My initial thoughts on the Rebellion have the same concerns that Gratz is voicing - it seems with all possible bonuses that the checks might become irrelevant. I know there are some limitations to number of teams and with some of the events where NPCs might be captured their bonuses go away until they are recovered. Still a lot of the static DCs of Organization checks mean they will become easier as the campaign progresses which seems a little counterintuitive. Seems like as things progress and the Silver Ravens become more of a threat, things should get more difficult. I'm thinking of maybe tying Notoriety score to DCs somehow or maybe allowing certain NPCs to apply their ability bonuses to checks the same way PCs in leadership roles add their ability scores.