I celebrate Marillion for not putting out the same album over and over. But I think there's a spirit, a core of the band that isn't what it was for the first five years. They were a "prog" band in every sense of the word; see the "Genesis" complaints (even though I always thought it was more Floyd than Genesis). Mark Kelly isn't a prog keyboardist anymore; in a real sense, he's a DJ, triggering sounds and what not. Look at the recent documentaries showing their prep for tours. His entire gig is really setting up sounds and triggers and samples. I think Holidays was the first real glimpse or insight into that.
I think the bigger shift happened with This Strange Engine, where they really seemed to start digging around for a new identity. But I can see what you mean with the beginnings being laid here. One of the guys mentions in the documentary that the lessons learned from HiE helped them make Afraid of Sunlight, which I thought was a little interesting. That is in many ways a less proggy album, but not exactly poppy either. It’s also one that was heavily influenced and steered by the producer for whatever it’s worth.
I can't remember exactly what the time frame was, but I think it was around this time where every interview (I'm being a little facetious, but not much) seemed to include a bit where they tried to show their bona fides by claiming how they liked Massive Attack as much as they liked Genesis and Pink Floyd. I remember thinking, "okay, I get it. Now get back to making music, willya?"
The funny thing about Mark Kelly, every now and then he tries to slip in some more proggy keyboard bits, and I feel like it doesn’t go over well with either the fans or the band (see Interior Lulu). I think he may actually be the biggest prog guy in the band at this point (maybe Pete too). Have you heard his Marathon album? It’s much more traditional neo-prog. But he is very much into the programming side of things as well. There is sort of a running gag in the band about his live performances as well (that he sort of mails it in is what I gather).
I’ll also say Rothery has had a big role in Marillion’s more programmed bits. He came up with the loop that started Splintering Heart, and he also programmed the initial drum loops that were the foundation for much of Anoraknophobia.
I've honestly stayed away from almost all the Marillion solo stuff; I don't know why, I've never heard it so I can't complain about it, but I'm a critical listener with Marillion now, and I do watch a lot of the behind the scenes stuff. I sat through (agonizingly!) about 30 minutes of a doc about Kelly programming his sounds and while I get it on one level - Tony Banks does the same thing - there are also moments with Tony where he's in another world just playing PIANO. I never get that from Mark Kelly. I could be totally wrong, I've never met him* but I get a different vibe from him, like he wants so badly to be liked and so badly to have his music hit the charts that he's not really invested in any one part of the MUSIC. Maybe I should change that idea. I know I had heard good things about The Ghost of Pripyat or whatever it's called (Rothery's solo record), so maybe I should be fairer to Mark as well. I just know that for me, the epic period of Marillion ended with Afraid Of Sunlight. I checked out with TSE for years (Estonia is really the only song from TSE I like) and only came back with Marbles, but they then lost me immediately with Somewhere Else, and have never really fully regained my trust. I do like parts of .com, the remix of Radiation is really good, and I dig parts of Anoraknophobia ("Separated Out" would be a top 15, top 20 song were we to do a countdown).
You talked about producers; it depends on WHAT producer. Bob Ezrin HEAVILY influences whatever work he does, but the albums are almost universally excellent, and bring out the best in that artist (Destroyer, Peter Gabriel I, all of Alice Cooper, Get Your Wings (even though he didn't get credit; he introduced the band to Jack Douglas and did attend some of the sessions). For me, I would pay MONEY to see Marillion work with Dave Meegan again. The albums he's done with them are usually my favorites, even if the styles are adventurous (like Anoraknophobia).