It's a problem endemic of professional rugby in the Northern Hemisphere to be honest. With the trials of a domestic season, a European campaign and a rake load of internationals all in the space of a few months it's very rare that any side can look to field its strongest fifteen more than a few times a season. The French do it by targeting games as you mentioned and it's a similar situation in the Celtic League. As ever, the good sides just have larger squads so the difference is less noticeable. For example, Sean Cronin coming in in place of Richardt Strauss isn't as big a drop off as Munster putting in Ivan Dineen for James Downey. If Leinster put out a side with Boss, Cronin, Ruddock and D'arcy in it one week and Reddan, Strauss, McLaughlin and McFadden the next you'd struggle to call either the definitive starting side.
I suppose that's where the difference between the Celtic League and the Top 14 is showing at the moment. A bigger budget means that the French teams can afford larger squads, and as such their rotations aren't as galling.
However, I don't think it's a fatal problem by any means, at least not for the Irish sides. We're churning out far more players of the required calibre than we were even 5 years ago and that will start to show in terms of depth and therefore quality of the league sides over the next few years. As an example, if you'd told me in 2007 that Munster, Ulster and Leinster would all have young Irish 10's starting for them, as well as Johnny Sexton, Ian Humphreys and Gareth Steenson playing regular top flight rugby abroad I'd have hardly believed you.
There's plenty of reason for optimism about the Celtic League. Connacht and Treviso are both on the way up, Ulster have emerged as a serious European force, Munster seem to have sorted their academy problems, Glasgow have been performing consistently well for the past few seasons now, there are new lucrative TV deals with Sky and with an Italian company and attendances have risen from 2011/12. Admittedly, there are large areas of concern, particularly the Welsh attitude to the league, but the situation isn't as bad as it's being made out to be.