SQ5 actually altered Roger's character more than SQ6 did. Roger as presented in SQ4 is a doofus, self-centered and definitely the opposite of an alpha male. He even gets friend zoned by the Latex Babes. He clumsily saves the day. He's a goof. He's presented similarly in all the games except 5. And 5 is the only game written by Mark Crowe, who had mostly done graphics in the other games. SQ5 is a good game, I enjoy it, but it's more a parody of Star Trek than a SQ game. I never liked the idea of Roger Wilco as Captain, it kinda ruins the entire premise of the series (average Joe, semi-competent average Joe, saves the day). It'd be like seeing John McClane become Captain of the police force rather being than your average, borderline alcoholic cop; It ruins the everyman appeal of the character. I never saw Roger as this hero in the traditional sense of the word which SQ5 presents him as; he's more the right guy who happens to show up at the wrong time and gets wrapped into events beyond his control. I mean, in SQ1, we're told he's not even a competent janitor who would've been sacked if the Arcada had been nearer to home. He's not Captain material; and nothing in any of the other games ever suggested such.
I also feel SQ5 introduced Beatrice waaay too soon and hamstrung any future entries. SQ6 was a return to the series' roots, a return to form, and it features the acidic wit and writing of Scott Murphy alongside that of Josh Mandel. It was a return to form. The only downside of the game was the cliff-hanger ending, but who in 1995 could've predicted that Ken would suddenly decide adventure games were dead and sell the company off?