I've got both heroes and villains. Would definitely be nice to have some more strike forces, the ones we've got are pretty solid and fun and worlds better designed than several of the trials and task forces on the other side.
As for why it's less popular. Probably a combination of reasons, it really depends on the person. It's hard to make accurate blanket statements because there are dozens of exceptions.
For me? I do prefer blueside. I am a more heroic person in general, I like playing as the do gooder and beating up the bad guy and feeling good that I saved the day and stopped the evil plot. It's pretty easy and simple content to generate and even if a lot of the mechanics aren't always that fun it's not really the writing that ever bothers me. It's kind of a hero's role in life to ever be vigilant against the many and varied threats against the world.
Villainside... well, as has been said, more often than not you're treated more like an errand monkey than a super powered villain. They don't really have the freedom to pursue their own plans and the like, which is understandable given the limitations of the game's mechanics. And villains can't ever really 'win'. There's stuff where we get to feel like real villains but nothing that actually changes the status quo, even when we 'win' like Vincent Ross or Dean's arcs, things still hit back to before. And it's understandable, the game would be broken if we could really steal death rays and ancient artifacts of unfathomable power or could rob banks for millions of dollars. Our clone facility blows up, our shard of infinite power only lasts a single mission, we sell that priceless artifact for 1,000 inf, etc. There are always bigger, stronger, nastier villains out there whose plans get to come to fruition and we have to help or hinder them, but villains never get to be 'top dogs'. It doesn't really bother me, but it doesn't change the fact that Villains are always on a leash. And even when we do get some plots where we get to be the mastermind behind the plot, more often than not we get words put in our mouth. Really I don't envy the folks that write for redside, they have a lot harder job than blueside. Heroes are easy. "This is bad, you don't like bad things to happen" is the only justification absolutely -needed- blueside. Redside? What compels the character to want to do this and work for this person? Is that -too- villainous for my character? Not villainous enough? etc. The problems are legion.
The economy of zones is, honestly, kind of a hindrance too. I mean, it's nice there aren't any empty wasted zones like blueside, but at the same time my characters generally run about the same path without doing stuff like power leveling. The zones overlap a bit, but I still run the general chain along mercy->port->cap->sharkheard->nerva/martial->grandville. Not really because I want to, I just have to. I at least have the option of First Ward at 20 (though, how many times can you rerun First Ward?), but after that I generally find myself running up the same ladder, XP gains and levels come slower so there's a lot more room to do repeat contacts, doing multiple arcs and thus multiple contacts between characters (and fewer characters at that, due to Redside's intimate size). Even mixing in Cimerora and the RWZ, I still find I'm overlapping contacts. After the umpteenth run through, the scenery gets kinda stale, whereas at least Blueside I have several options available, I can go through king's row, I can go through the hollows, I can do Steel Canyon or Skyway, I can hit faultline, I can do Talos, First Ward, Croatoa, etc. It doesn't really start to collapse together until I hit Peregrine.
There's also the minor problem of locked contacts. I kinda like the idea of earning contacts via different requirements, but there's more than a fair number redside (In fact I think almost all if not all locked contacts are redside) and unless you know about them, what their unlock requirement is, and actively pursue it, more often you'll miss it. Easy example, Archmage Taraxis, super easy to unlock, just a history badge. Unless you wiki it you'll never know that and won't know where to find any of the plaques except by some very meticulous checking. As far as I can tell, there's nothing actually in game that tips you off 'hey maybe you should get this badge' etc.
Speaking of, blueside is -super super- easy on contact chains. In fact it's kind of hard to be without a contact at any given point in the game. Even if I outlevel a contact before even talking to them they'll still usually shoot me to someone else. Redside I'm pretty much required to repeatedly hit up brokers and newspaper missions to get new contacts.
And I've found redside content to be a little harder. Given, I'm still green comparatively. But I solo heavily and just from personal experience it seems like villainside missions are -extremely- prone to throwing bosses and elite bosses at you. I mean heck, compare the Shining Stars Arc to the Hearts of Darkness tutorial arcs. Most missions in shining stars when you face down multiple bosses in the same mission you have 1 or more allies. hearts of Darkness? Most times you don't. Sometimes you even face down two bosses at once. That can be kind of offputting especially when you're something squishy like a blaster or dominator and don't have all your tools yet.
And then there's just some of the weird stuff like the accolades for the different sides. Atlas Medallion is stupid easy to get and early on at that. Marshal? Gated behind the Lord Recluse Strike Force so distinctly endgame. Task Force Commander? Not that bad, a bit tedious but you can get it as soon as you can access Numina. Invader? Oh sorry, you missed that Mayhem mission, out of luck unless you port to blueside and nab TFC or get supremely lucky and join someone else doing that mayhem mission (Hope you're not a Praetorian btw!). Super tedious. Portal Jockey? Again all roads lead to Peregrine blueside, it's hard -not- to do Maria Jenkins and Tina Macintyre. Born in Battle? oh, gated behind a random GM spawn and having to take 1 million damage. You'll get it eventually but, eh I'd rather just do Maria's arc with friends (And I can solo the arcs, can't solo Scrappy). Phalanx reserve? Tons of Exploration and history badges, 2 pretty easy defeat badges and the Nemesis defeat badge, a bit tedious and can be hard, but easily doable. High Pain Threshhold? Best work on that debt badge!
Though they do have some weirdly easy ones, like Demonic is -waaay- easier to get than Archmage, or something like Force of Nature. But for the most part, not the case.
I do kind of like that Redside's GMs are actually a lil important, since pretty much all of Bluesides are just for the badge (Though Adamastor's revamp has been -quite- nice in terms of rewards). But Scrapyard can definitely be a pain since he's on a fixed timer and you -want- to pull a team together for a GM fight.
That said though, the redside Strike Forces, for however many there are, are actually pretty fun and worth running, nowhere near as tedious as a lot of the blueside task forces and trials. Honestly Mortimer Kal is one of the funnest team events in the game, not just for the really nice reward but just it's extremely enjoyable to play through. Missions are varied, not too long, not too hard, the story is kinda interesting, the maps are neat, etc.
So yeah, I enjoy redside for being different, I mean I'm paying for the game, I'm going to enjoy playing all the content. But honestly I do prefer blueside.