Actor Kevin Sussman reveals that Stuart was secretly in love with Penny (Kaley Cuoco) to the end of The Big Bang Theory. When the CBS sitcom debuted in 2007, it initially had five main players — Penny, Sheldon (Jim Parsons), Leonard (Johnny Galecki), Howard (Simon Helberg), and Raj (Kunal Nayyar). By season 4, Amy (Mayim Bialik) and Bernadette (Melissa Rauch) were promoted to series regulars. But before they even joined the show, it already had another semi-regular character in comic book store owner Stuart Bloom.
The character was a talented artist; he originally wanted to be a comic book illustrator. But after realizing how impractical it was to blindly chase after his dreams, he made a compromise by starting his business selling comic books. Stuart regularly hung out with the Pasadena gang and even became particularly close with Mrs. Wolowitz (voiced by Carol Ann Susi) after he was hired to be her temporary caregiver. While he's not technically part of The Big Bang Theory's main cast, he's often dubbed the sitcom's eighth main character. Stuart was consistently invited to several personal events, such as Sheldon's birthday and Leonard and Penny's wedding - although attending the latter may have been very difficult for him.
While at Roster Con, Sussman talks about his role in The Big Bang Theory. He reveals how his attraction to Penny started after an improvised line, which was then adapted into future storylines. Interestingly, he says that Stuart has an "undying love of Penny," which means that, until the very end, he was still carrying a torch for her.
There was a scene with Penny and she is, she comes into the comic book store and she asks me a question and as she's leaving, I - which was not in the script - I muttered under my breath, "I love you." [...] And from that point on is when they started, they sort of caught on to this whole Stuart vibe where Stuart sort of regresses, because he started as a normal person and then he gets more and more desperate and his undying love of Penny.
Penny and Stuart briefly dated back in The Big Bang Theory season 2. In fact, he even scored a second outing with her, implying that she might actually be interested in him, although he didn't necessarily fit the type of men she usually went out with. Her decision may have had something to do with her complicated romantic relationship with Leonard. Somehow, Penny might have realized that it could be better if she hung out with nicer guys like him and Stuart. That romance didn't last very long, however, and it was never revisited in The Big Bang Theory. Penny went on to get back with and eventually marry Leonard, and in the finale, they were happily expecting their first child together. Stuart, meanwhile, was steadily dating Denise (Lauren Lapkus), so it's quite surprising to learn that Stuart was actually in love with Penny the whole time.
Speaking of Sussman, had the casting of The Big Bang Theory panned out differently, he may have ultimately played Sheldon. He could've played the part opposite Barry Kripke actor John Ross Bowie, who auditioned for the role of Leonard. Obviously, that didn't materialize, but it didn't seem like either had any ill feelings about not getting those lead parts. In any case, Sussman was as good as a mainstay in the show, appearing in a total 0f 84 episodes from season 2 to season 12.
Source: Roster Con