Fact is Slave, whether you accept it or not, there are a lot of fans who feel or have felt like IF disrespected them with their words and decisions post-2000. That's why there are hardly any proper older fans left, and there is so much spite towards them online, way more than any other comparable band from that era and genre. IMO it's also part of the reasons their popularity nosedived after Come Clarity, but the overall quality of records like ASOP and SC also played a big part in that.
I personally don't feel disrespected as I only started buying their stuff after they started breaking away from the undergroud, I wasn't one of those guys buying their albums when they had just released Lunar Strain, TJR or Whoracle. By the time I really started getting into the band they were already getting shit on for Clayman and then even more with Reroute. That said, I do understand why people would feel like IF gave them a middle finger after they helped support them. They basically did.
I don't think fan appreciation has much to do with being super popular or not. If they like the music, they buy it, and go to their shows, if they don't, they don't. Trust me, 90% of the people who buy records, merch and concert tickets have no idea what Anders says on twitter or in other interviews.
The fall-off after CC can also not be because of the olds fans, because their popularity was payed by the new fans. The R2R-CC era brought in more new listeners, than they had before their entire career, so even if they were to publicly burn TJR, someone who fell in love with The Quiet Place would not give a fuck about that.
Also, after you reach a certain level of maturity, you have to accept that even famous people are just humans, thus assholes. Most importantly, they are not your friends, and even if they tried to be, they simply can not be. If artists like people in IF want to keep their sanity, they have to ignore you and me.
And yes, the reason their manstream popularity dropped was due to the changes from ASOP onwards. As I said, ASOP was a really fucking good old-school record. But the people of R2R-CC never asked for it. They liked an In Flames where Anders screamed his lungs out, and the music was fast, agressive, yet commercial. ASOP is extremely non-commercial, with the exception of Alias. It is really hard to show down on the throats of radios. The guitars are really cool, but where are the catchyness of "if iii eeeveeer, if iii neeeeveeeer" ?
Then they started to play rock music, which sealed it. But it's okay, "no king rules forever", plus even before the R2R-CC era, they could not have known that they will be this popular. Especially with R2R and CC. If you actually KNOW before their release that those records will be commercially successful, then you should do lottery. Even if you accuse them of trying to copy the hip American metal elements, just compare anything from CC to stuff like Breaking Benjamin or Linkin Park. Not exactly target audience.
Personally, I am happy that they sticked with their guns even when they were at the top. It is easy to say that you change your music because you always want to play something a little different when you are just some C or B level artist. But when you hit the jackpot, that is when you have to put your money where your mouth is. And they did. And I can respect that. That is integrity.