There are several factors that could be considered in an explanation, but the most important and and simplest one is this:
Here's another way of looking at it: Dark energy (being as near as anyone can tell a feature of all vacua) is just an extra term in the gravitational metric. So if attractive situations in the field dominate then things move together (eg Andromeda toward the Milky Way) and if the field strength is very low (out in the middle of nowhere then you get "expanded vacuum"....
While the universe is homogenous when taken on a large scale, this isn't true once you get really local. That is, while matter is--more or less--evenly distributed throughout the universe, you will still have areas where matter is more concentrated than others--galaxies, galaxy clusters, superclusters, etc. While the universe is expanding on the large scale, gravity can be the more powerful and dominant force in these local interactions.
Personally, I'm not convinced that space is expanding or that there is dark matter at all. This is not the first time that learned people have observed a phenonemnon and fabricated an explanation that turned out to be wrong. And they have a nasty habit of killing people who don't agree.
The only evidence for expansion is red-shift. No matter what direction you look, everything has a red-shift. And the farther away it is, the bigger the red shift. So, the farther away something is, the faster it appears to be moving away from us. The only explanation that fits is universal expansion. But isn't it possible that these red-shifts could be caused by something other than recessional velocity? We've only known about red-shifts in stars for a hundred years or so. And man thought the Earth was the center of the universe for several thousand years before he figured out it wasn't.
As you pointed out yourself, though, it's the only explanation we currently have. It fits the observations, and we can make models and predictions from it. It may not be perfect; it may be completely wrong, but that fact is that it's the best thing we've got. I understand your skepticism, but I don't really think "because it might be wrong" is a good enough reason to dismiss a very good explanation.
Until someone comes up with new, experimentally testable physics that would better explain the observations, most of us are going with an expanding universe.
So, galaxies colliding is no big deal. We have pictures of it happening, after it has happened, and about to happen. Shelve expansion and dark matter and let your mind wander! Come up with your own explanations for the phenomenon we see, they are valid as any other.
It's great to come up with one's own ideas. I've had a few of my own. But any idea would still have to have a lot of mathematical rigor, observational evidence to back it up to be anywhere near as valid.
As for dark matter, the idea of the ether has only been dead for about a hundred years(Michaelson Morley Experiment) and now it has apparently been resurrected! Amazing how science, which claims to be totally emperical, and often denounces those who believe in the spiritual, will simply invent whatever abstractions are necessary to prop up a popular theoretical framework. No one has ever seen dark matter. Never measured any. We know NOTHING about it. Yet it's existence has already gone past theoretical and become accepted. Faith? I guess scientists have it too.
I think you're getting a little carried away here. Dark matter isn't really like the "ether." Nor was it invented to prop up a merely "popular theoretical framework." General relativity is as good as we have right now for understanding gravity, and I'm guessing that would have to be the "popular theoretical framework" to which you refer. General relativity may not be perfect--hell, it certainly won't be close even, and neither will QM, until we can unite them--but it's extremely rigorous and has proven itself time and time again with observation and prediction.
Yes, "dark matter" was invented to explain the differences between GR's predictions and the observations in the velocities of outer stars in distant galaxies. The "missing matter" hypothesis was the best, unless there is a problem with general relativity--which there may well be. But with its track record, the more likely explanation is some kind of weakly interacting massive particles, or some other form of "dark matter," non-observable but through their gravitational effects. I'd hardly call it "faith" when one's belief is based on observational evidence and the scientific method.
While physics sure has had its share of embarrassments of scientists clinging to outdated ideas they believed just
had to be correct, out of some faith or ego or intransigence (e.g., the ether, or even Einstein's rejection of QM), it's also had its share of discoveries through exactly these kinds of theoretical "inventions" and hypotheses. The positron, for instance, was theorized in a similar way--as a hypothesized particle naturally arising from a certain theoretical framework (the Dirac equation). No one knew whether it existed or not; no one had seen it before. Lo and behold, some testing later, and it existed.
No. We don't know what dark matter is. Does that really matter? We see its effects. We can measure them. When a better or clearer explanation comes along, we'll adopt that. But for now, they "dark," or unknown, and what appears to be "matter," and ultimately, that's just place-holder until we know what the heck it really is (or manage to explain it away through revision of GR).
Skepticism is good. But sometimes it's easy to get carried away and dismiss good ideas.