You are correct, the House of Stuart was not a shining example of peace and tranquility. Then again neither was the House of Tudor nor the last 100 years of the Plantaganets. Combining the religious conflicts between Catholics, Anglicans and Puritans with the growing power of Parliament at the expense of the Crown, it is hard to imagine that any dynasty would have faired much better.
It is also true that there were a great many Anglophiles in Scotland- especially south of the Firth of Forth. Many of the Scottish nationalist rebellions could also be characterized as civil wars between the Anglophiles and Anglophobes- much like the Carolinas during the American Revolution.
Well, I agree in principle with the statements made on this board that there is little point in refighting the battles of the past, especially as the reasons for fighting said conflicts may very largely have disappeared, or at least radically changed. Nonetheless, the past MATTERS. All modern nations are, after all, the sum of past events, both good and bad.
As to the original question, my own personal thought is that the Union is indeed tottering. I am sure it will see its 300th birthday but I also think it very likely it will collapse in my lifetime. On the one hand, I can accept that with some "sang froid". 300 years is a long time for a country to exist. There are not that many nations, especially modern nations, that last that long, even those we think of as being "old". The French (who in all senses are a pretty revolting lot) are on their, what, fourth republic since 1795? Norway is only a century old, Italy only a little more.
On the other hand, I live on the borders. I'm very conscious of the past history of England and Scotland. The border wars were not pleasant, in any way. The ultimate lesson of the low-level conflict that we had to live in prior to the Union was that this island is too small for two government, or at least it was in the 16th century. We can only hope things can be different now.
Personally if Scotland does gain independence I'd want to come with them. My impression (and I may be very wrong here - the Scots of a nationalistic persuasion on the board may correct me) is that Scots Nationalists are not so much against England as against London, an attitude most in Northern England would share.