I never mix lines because the clash of aesthetics doesn't work for me. Even to the point Siege figures haven't really met Prime Wars ones yet. I like the TF4 Dinobots but I don't actively hate the Bay films. I'm kind of ambivalent to them really.
When it comes to the Unicron trilogy, I'd have said the toys are the source of the cartoon rather than the other way round, but I like both. I can't think of anything I own that comes from a source I really don't like.
I'm only interested in the toy design nowadays. I was a pseudo-completionist during Beast Wars, Beast Machines and RiD, buying almost everything I could find unless it was really, really bad (like tall Cheetor). Armada's blocky & simplified toy design convinced me to switch to a 'Significant characters and toys I liked' approach (with the occasional rash decision), before gradually switching to an 'only toys I really like' approach over time due to space limits.
A low opinion of a series or character portrayal doesn't put me off a toy - I bought the ROTF Autobot twins and still believe they are good figures! I do occasionally buy toys I sort-of know I'll dislike simply because I like their character though (have I mentioned how James Roberts appeared in a vision and forced me to buy Generations Whirl?). I'm trying to stop myself from doing this in the future.
Most of my toys stand in their respective toyline, grouped by faction and team. There are a few G1-esque Movie-line figures in the Generations display, like DOTM Shockwave (who will be moved if I get Siege Shockers), ROTF Skids and ROTF Sideways (both of who are Invading Zombies at present). I'm not anally retentive about grouping them by their source line. It's just that, as people have said, each line has a distinct aesthetic and it looks odd if you mix them.
It's a funny thing for me, I used to be all about nostalgia and being a completionist, but one day while going through my collection I realised I had a lot of figures I actually didn't like. And as the result of me moving back to England and having all my worldly possessions reduced to two suitcases and a carry on, which to be fair were more toys than clothes, I shed all the figures I didn't love. This set me with a(n) (almost) clean slate for collecting.
I grew up in the 80s with the original cartoon and saw the movie in the theatre. Although I didn't get into comics until later in life as comics were contraband at home, so never really got into the tf comics until very recently.
I have always been a con fan, but collected both sides.
As time went on I realised a few things, I in general like toys, I especially like monsters and robots. I really like a well designed toy, especially if it has good articulation.
What I discovered is that I do love the tf franchise, but I also like cool robots.
Now, I only collect and keep figures I activity like. I still keep watch for good representations of characters I like, but if the only option of a character is a poor one (imo) I don't get it.
Also if a tf figure is well designed, or just plain cool, I will get it. Even if the line in general doesn't interest me or even if I dislike the character.
Extreme examples of separation for me would be rotf megs, I love the crab tank megs. I have the several voyager rotf megs, including a couple of the ss rotf megs, just such a cool monster robot toy. I am always working on conversions of this chap.
Which I guess is my point. Rotf voyager megs, including the ss voyager as well, are in my collection for sure, but they don't stand with my tfs, they live in the cool robot horde. Rotf megs is very cool, but 100% NOT MY MEGATRON. So in this case the figure has been completely stripped of his official transformers status, but instead has become a separate (but important) entity in my collection. And to be honest quite a lot of the bay verse lives in this non tf but cool robot horde.
It seems in my case, I am more about cool robots, than hardline transformers.
But then again, I have never been a good collector, I always swapped weapons and accessories to suit my desires and aesthetics. I even happily swapped factions to suit, my ram horn and steel jaw were (and still are) cons as sound wave deserves ALL the best minions!
And, I have always been a tinkerer, parts swapping to get better aesthetics or mobility, tearing out "action features", and never being squeamish to take dremel and file to "improve" a toy.
So I guess the seeds of toy first were always there, it just took a while to grow.