I think it's obvious that the relationship aspect wasn't an integral part of the show until much later around maybe Season 3. They planted the seeds for it if they felt like pursuing that story, just like with anything else in the show. If you don't like that, then Adventure Time is obviously not for you and, quite frankly, if your main critique isn't how they handle the overall story writing, your opinion doesn't matter.
They made the story up as they went along, and M+P was no exception. I don't see why this is a bad thing though. I think the episode "What Was Missing" perfectly sets up Marceline and PB's dynamic. They had already been on less than friendly terms and their personalities often clashed with each other. Considering they are immortal beings, it makes sense to me at least that they might go through periods where they like each other and others where they can't stand each other. Opposites attract is still a rather a popular cliche and one that's my guilty pleasure.
It's not like they are lesbians either. Princess Bubblegum has shown interest in men (well males) before, and Marceline likewise, even after 100s of years.
I genuinely think they were going for a low-key approach to the whole thing, because a whole episode over their relationship would have been too easy and probably not very interesting. PB is shown to be very above romance, and Marceline became a lot more reserved as the series went on. I think it makes sense they'd keep things hush hush because there are more important things in-universe to worry about.