When I think about the editions of DnD I enjoyed most, 1st, 2nd and 4th edition I realize that they do things that are distinctly illogical a lot of the time from a "reality" point of view. 3rd edition tried to do a lot more, for example the inability of rogues to gain sneak attack damage against undead, plants and constructs for example was logical. When I first played 3rd edition, I thought that was a fantastic and logical addition to the game, because it just made sense in the end and supported the concept that dead things didn't have anything truly "vital" to attack anymore.
Over time running 3E I noticed that the guy I had in my group who played rogues/thieves since 1st edition had absolutely zero fun because he was utterly useless 90% of the time in my undead heavy campaign - while spellcasters were anti-everything can openers and the fighter wasn't penalized any while we're at it - I started realizing something wasn't right here.
This is ultimately why I like 4E, because I prefer conditions to be universal and exemptions to be just that - not something that is normal or even based on a racial trait. It's just something that fits that monster specifically and makes it unique/interesting. If you can't knock something prone, it is because it's a particularly significant monster - not just some creature type we've determined should be immune. This means powers can be designed and work consistently over the whole game. Rather than needing to note their numerous deficiencies when you have different monsters.
This is why we bring up the grapple fighter, when you start ruling a bunch of stuff ceases to be grabbed you make an entire interesting, balanced and fun build in 4E absolutely useless. I mean why stop with swarms? Insubstantial creatures? Creatures that can phase? Creatures that are significantly bigger than you are? And such forth.
Realism doesn't go well with balanced rules IMO. I prefer consistent rules that make for a fun game, over "fluff based" rules that make someone wonder why they bothered turning up to DnD that night as they're completely useless.
2 things strike me each time I hear this. First is that the whole "my grabby fighter will be worthless" is just overblown. In fact it was just an easy example that everyone already had in mind. We could easily talk about ANY build of any class in this vein. You can see where the reductio ad absurdum comes in here, if there are a few times when each character's specific shtick is thwarted then they're worthless? I guess ALL THE BUILDS IN THE GAME are worthless then. Obviously there is a serious flaw with this logic...
Secondly we aren't talking about something that happens ALL THE TIME. You're entirely correct, 4e has cut way back on the "it is immune to X just because we think that makes sense" thing. However, they haven't entirely, by any means, eliminated these kinds of things. They're not just annoying badwrongfun either, there is actually a good reason to have them. They allow different monsters to be more unique and interesting. What was wrong with 3e's "you may not backstab undead" was it was WAY too broad. Sure it made undead 'different', except undead are all over the place so they really didn't need a way for them ALL to be unique together. It is much more interesting if different monsters have different quirks. So big deal if swarms (a very rare monster type) can't usually be grabbed? It isn't even a blanket proscription.
As for the 'it will just spread like a virus throughout the game', meh. There is already a rule that you can't grab anything more than one size category larger than yourself anyway for instance, so this is hardly a big concern in that specific case. It isn't really clear whether a phasing creature can or cannot simply escape a grab, but there's no reason to suppose it can since it actually can't move through your space either IIRC.
My point is that the basic default ways things work ARE the best. That doesn't mean you have to slavishly adhere to them every single minute. It just means you should keep the variations to a minimum. So for instance the phasing creature can be grabbed and held because well you "can't phase through flesh" (if you need fluff for it at all). It just an exercise that the DM should be performing in his head as he runs the game, asking what will be interesting, logical, surprising, and fun.
It isn't always the most fun for things to work like X just because X is RAW every single time. Players actually LIKE to be presented with quirky challenges sometimes. You guys all act like someone spit on your mother if you're character doesn't get to do his thing EVERY SINGLE round of every combat. Knock it off! It is MORE FUN if once in a while you run into "oops! Oh Crom, now what do I do!" here and there. Call it arbitrary all you want, but when done well it is quite good for the game, just like it is often quite good for the game to give away the treasure you WANT to give away and not fill out checkboxs on Joe's wishlist all the time, etc. Half the wonder and fun of the game is stuff that you don't expect and weren't ready for.