A lot of the Cilan love just stemmed from the fact that people were glad Brock was finally gone. I don't need to remind everyone of how DP Brock was received.
Clemont's popularity depends on how he is received later in the saga.
So in other words your implying how Cilan was viewed as "consolation prize?
Apology for "terrible character named Brock"?
Note: i dont consider Brock to be bad character at all.
How well new characters are received depends on what kind of personality, interest and background he has. What role he performs and his value in leaving impact on plot and other characters. Cilan was well received on his own merits, not because he replaced Brock.
Also vocal minority which was happy over Brock leaving dont represent general consensus amoing fandom. Because all i see is only increased interest and desire from people on numerous sites that Brock comes back displaying how there certainly exist sizable portion of fans which like this character.
Same applies to Clemont, his likability isn't conditioned by who he replaced but in how engaging and relevant he is going to be to Kalos series. Whether his hobbies, interests, characterization and way he deals with other members of cast accompanied with plots centered around him makes people to start symphatize, care and enjoy in his presence.
Personally im not that much worried about Clemont future at all. He has great chemistry with his sister being very caring and considerate about her, see somesort of role model in Ash admiring his bravery and compassion toward pokemon. Comes up with various strange devices and inventions which dont always backfire helping to advance plot(like for example in saving Ash from falling from building with his air bag, helping Ash in training his pokemon for rematch at Santalune gym or retrieving some of lost energy for Dedenne),
Even after his long awaited battle against Ash for 5th badge comes , which i presume would be feasible way to put to test how much his traveling and hanging around Ash helped him in improving skills and bringing more creativity strategy wise i wouldn't be worried in slightest over his role beginning to fall afterwards.
Having potential and space in his story to expand upon. For example there is whole connection between him and msasked mega Blaziken guy who happens to be Limone(his own fathger). Opening reasonable hypothesis over Clemont playing important role in future events centered around mega evolution, Limone and even Team Flare(since one of their main activity lies in exploatation of mega evolution to their own benefits).
Perhaps mega Blaziken man might be on undercover task or some sort of detective , investigator researching increased activities of Team Flare as part of anti crime organization whose aim is to stop them. Leading to possible misunderstanding between father and his son Clemont due to at first wrongly reading in his motives and actions taken regards villains not being able to realize how he is on side of good.
Such kind of plot twist probably wont happen, but there definitely exists ways to keep Clemont infiltrated within main storyline and keep progressing character wise after revisit of Luminose city.