Gwent is unpopular, because HC shocked most of the playerbase back then. SOme for the content-change, some other for the very poor communications. Honestly, i never was in a game forum with so less and poor communications. They onl addressed some negativ feedback, if they have a change in mind; only happy-telling.
They wanted to recover from this shock, but failed. Why? Becaue the New-Game wanted to be a bit more casual, with reduced cardpool, row and archetypes as well as mechanics in general. They slowed it down further by adding charges and orders. Gwent was a relativ fast TCG, compared to others. This was a unique selling point (for all those, who stayed). It was fast, but not without depth.
The new game was far less deep but slower, the most time is taken not by thinking but by clicking. It wasnt simpel any more, nothing you couldplay in a 10 min break.
For all players who love slow gameplay it lacked in depth. If you want to think about something there should be a point beside just math.
For me, gwent was dead with the new 2 row system. They threw all relations to original gwent away. It was a logical step at this time, i admit, because they "smoothed" the rows for a long time now, till they lost all meaning. It would have been easy to get some depth back with a 3 row-system +reach+hard placement (=/= agility to all cards).
For Background: I never played really competitive, reached rank 2100 once i guess. But i had fun at the lower tiers with my own themed-decks, and thats teh different: I hadn't fun in HC with it. All i tried was helpess staleness for me. I had no chance against a standard deck (= just just standard 2-3 cardcombos which generate much point) only against brothers in mind theme-decks or try-out decks it was fun. And at top, i was matched against counter-decks 90% of time. (For example, i was crushed by artifacts the last 10 games, so i wanted to try some minorartifacts i had to. The next game i was facing the first deck with anti-artifact cards, i ever met...)
In my opinion you cant say, why Gwent isnt popular without seeing it's history. Maybe it need changes, but the ones it got, were the wrong ones