I agree that the costs of developing a Breakthrough are rather low. My own analysisshowed that an Hermetic Brekthrough can be most efficiently achieved in 28 Warping Points [but 95 Seasons, the researcher is going slowly], on average.
The issue is one of playability and fun. What is the role of Original Research in the game?
I think there really are two roles. One is to establish the character as a theoretical genius and to allow for political machinations around the fruits of his work. This role is served well by Minor Breakthrouhs, which do not unduly upset the game and allow the magus to develop House Acclaim. In order to serve this role Minor Breakthroughs need to be relatively common, so that it would be reasonable for the PC to develop one. Even a relatively young but talented one. This implies, to me, a cost of a few years of dedicated research, and I think the costs for the specific breakthrough sought should simply be set accordingly - set the number of stabilized magnitudes to be whatever is needed for the PC to achieve this in a few years of dedicated research. In principle, there should be a store-house of such minor, easily-integrated virtues available to the Order; presumably most of them quickly get integrated into the general Hermetic theory, so that indeed the modern Hermetic theory isn't quite what it was a few centuries ago.
There is a natural tendencay to desire more, to desire to achieve great fame and break the limits of magic. In other words, to achieve a Major or even Hermetic Breakthrough. As much as I like lab-work and number-crunching, I think this works best not as Original Research, however, but rather mainly as Ancient Magic. Particularly large and impressive breakthroughs should be discovered mainly using about two or three sources of Insight - even Bonisagus improved his magic theory with the aid of the other Founders! Stories are just a vital part of Ars Magica, and I don't think they should be abandoned. By keeping the sources of insight insufficient in number, theorists retain their usefulness and role as even after all the insight has been gleaned long years of research are still needed, allowing for political machinations in light of the looming breakthroguh. Again, the costs should be set accordingly, but this means the basic cost of a Major or Hermetic Breakthrough should be astronomically high but would be cut down by a few potent sources of Insight to such a level that a few decades of original research would suffice; perhaps a single decade or two of original research, plus sources of Ancient-Magic Insight, then.
The second role of the original research mecahnics is to provide a means to obtain a character goal - e.g. discover the secrets of creating regios, or so on. I think this role is served well by my reasoning above regarding Major Breakthroguhs, and should be treated as such.
I see no real distinction between Hermetic and Major Breakthroughs in that regard. Both are essentially there for the end-game.
In terms of setting realism, under this structure there would be very few Major/Hermetic Breakthroughs as a) the costs are per-breakthrough so really it's a matter of SG-fiat, and b) the costs are very very high so the discoveries can only be achieved by the SG deciding Ancient Magic has been found to speed up the process (SG-fiat again) or by multigenerational, probably House-coordinated projects.
A third role, acquiring virtues and power, isn't worth discussing. You're better off chasing mystery cults or forest paths anyways.
I would, BTW, not adopt the Original Research rules as they are. I'd suggest adapting the Ancient Magic rules; I've presented my own suggestion on how to do that here.