A long rant about Westerosi politics
I think from a meta-perspective, I'd actually have to disagree with The Drunkard. Targaryen rule was neither good nor bad in my opinion- save for the Night's Watch and Ironborn, and what it did was tone-down a lot of widespread medium-intensity, local warfare into brief but high-intensity, realm-wide warfare.
I base this on the fact that, from what we can gather of the pre-Conquest period of Westeros, its political and power structures seems to have been operating in a realist kind of anarchy. In this scenario, each major power (in this case, the Six Kingdoms and Dorne) probably had sort of a core territory of loyal nobles, and a periphery of nobles constantly changing sides in the never-ending ebb and flow of warfare. There's explicit reference to this in the books, with mentions of the The Riverlands (which also included the Crownlands at the time), the Stepstones, the Sisters and Dornish Marches; all being contested territorial areas, while mentions of Theon Stark, the "Hungry Wolf"- who put his people through so much war they were constantly starving, the Blackwood-Bracken feud, the Ironborn ruling from the Arbor to Bear Island, serious fears of Argilac about Black Harren gaining ground on the Stormlands, etc. are actual acounts of the conflict.
The reaction of the King Lommen and King Mern to Aegon's Conquest further supports this imo., since there's little evidence in both the books and in Dunk & Egg to Lannister and the Reach having any special historical ties that would make them natural allies. Rather, they formed an alliance out of an extraordinary perturbation of Westeros' balance of power during Aegon's Conquest, something they would otherwise be unlikely to willing to cooperate on.
What the Targaryen hegemony did for Westeros was eliminate this anarchy and provide a structure through which interregional feuds could be negotiated through (i.e.appealing to the King). Also, theoretically, it provided collective security for Westeros both from external invasion (via. Wardenship, such as during the War of the Ninepenny Kings) and internal rebellion (i.e. how all the Houses came together twice to squash Ironborn rebellions). It did however break down a number ofngs times, and most notably during royal succession (Dance of Dragons and the Blackfyre Rebellion being the worst). By nature of being run by despots, when they're enlightened rulers things go ok but when things get bad (such as with Aegon IV or Aerys II) it results in much bigger
wars than Westeros was used to; since unlike before, where only external threats to the balance of power could compel rulers to cooperate, internal
threats created by secession crises brought about war. And they are obviously more frequent during the Blackfyre realm than in Westeros (at least since the invasion of the Andals nearly a millenia ago, if the timeline is to be trusted).
Now is this good for Westeros? In some areas yes, in others... no. I think with a pre-Conquest system of localized despots working in a balance of power, which Robert ironically catalyzed when he took over the throne, can work; but since it's been interrupted, the result is the horrors of the War of the Five Kings. It results in near constant low-level warfare, but there would likely be few big wars (created only when one power gets big enough that everyone else threatens to squash it). The Targaryens squished a lot of the localized conflict, leaving only intra-kingdom conflict (like the Reyne/Tarbeck rebellions) and preventing the kind of endless, low-level warfare that dogged Westeros for so many centuries. However, they also created a situation where big wars are more likely to happen- and that has proven horrible for generations that have to deal with it.
I wouldn't characterizing Targaryen rule as "bad", it just changed the rules. What the Targaryens were bad at was longevity and planning; constant interbreeding obviously has helped insulate a lot of mental instability within Targaryen rulers, and the chance of one of them slipping up and pulling an Aerys made them problematic. They're also probably solely responsible for the degredation of the Night's Watch, since the dearth in never ending warfare drove their recruitment levels down to unsustainable levels. But, bad? Unstable perhaps, torn apart by structural forces within Westerosi politics- but they were obviously good for a time, and the reigns of certain kings (Jahaerys I especially) were glorious periods in Westeros' history.
On topic (
I would agree with OP though that Robert's rebellion was tragically necessary, but very short-sighted- both on the part of Robert and Rhaegar. On Robert's part, it seemed like, in order for his rebellion to be successful and last long-term, he would either have to abdicate his claim to the throne in favor of a new, manipulable Targaryen claimant (Viserys or Aegon) that he could force to do his bidding and dispose of later (as Littlefingermight) or pull a Tywin and annihilate the household completely. He settled for the latter in lazily done and incomplete fashion, earning him the scorn of Dorne in the process. The brutal way in which he reacted to Aegon and Rhaenys' deaths also drove Ned away from him, a long-term ally, as did his mistreatment of Stannis (both of whom make for poor politicans but good allies and yes-men at court). His indulgence in Tywin Lannister's gold left the kingdom brewing in debt and gave the Lannisters cause to install themselves in KL- and his complete and utter disregard for his children left him failing to see what Sansa, Jon Aryn, Littlefinger and many others did; that something was amiss with his children.
On Rhaegar's part, from what we know of him he was well-liked, honorable and an overall upstanding citizen. However, I have my doubts that'd be any more an effective ruler than Robert. We're lead to believe by Maestar Aemon that Rhaegar was a rather quiet fellow who came to decision without consultation and little discussion (starting with him wanting to become a Knight one day after having read something in a book). He is indeterminate and rash, abducting (either willingly or unwillingly) Lyanna Stark after a Tourny attended by all the realm- and in Jaime Lannister's PoV, it's possible that he may have been implying a plan to depose his father (possibly confirming Varys' whisperings to Aerys). But it all came too late. He also tried to face Robert in combat; which, even for someone like Rhaegar, must have been crazy. Ned couldn't even lift Robert's warhammer, and he was something like a smaller but fiercer version of Gregor in his youth. It'd be like if Rob gave in to Jaime Lannister wanting to "settle" the rebellion with him one-on-one.
However, with the both of them acting like idiots (in 20/20 hindsight) and Aerys' mad execution of Rickard and Brandon, it became wholly unavoidable and one side was going to end up losing big-time. It was an all around lose-lose for the realm, the way it happened.