The plot of RBY's villains may seem very linear but on the face of it - it's easily the most believable.
Every team that has followed Team Rocket has been fronted by a mad man with unrealistic ideals and insane desires. All Giovanni was motivated by was money and power.
To be fair, a person with respect for either or both would not become a criminal - if they value power as such then they aren't subverting it -, so there was perhaps a bit of crazy about Giovanni. (Going into external media, Giovanni is shown as just as susceptible to playing with forces that he can't control, not to mention Team Rocket seemingly being holed up in a tower full of apparent ghosts, guarded by a ghostly Marowak.) There's also usually a bit of subtlety to them - for instance, most players (or you could say all of them) being shooed effetely from Celadon's gym, there's a secret entrance to the casino, and likewise their major schemes in G/S/C involve on the one hand a scheme involving 'Slowpoke Tails' reminiscent of the Magikarp salesman, and on the other hand turning everything into Gyarados, as indeed people tend to dislike Magikarp prior to this and hence the Magikarp thing seeming a scam, which is an interesting detail.
That said, if we're talking about being something seen as villainous, obviously at that time things with 'ideals' (and Magma for instance could only loosely be said to have such concretely, they were just attempting to make incremental improvements ultimately to shift things into a somehow better direction) were more alien and feared by people who associated it with crime than just the people working within the categories of society at the time, and in that sense TR were more anathemised for their slightly ruthless, ideal-driven edge than because everybody disliked and was supposed to dislike money, and related categories at that time.
I would agree on the 'believable' aspect to some degree, but perhaps mostly because TR's actions are most integrated into the game and its progression, while the later games took on a more cut-scene-based modus operandi (pardon) and this meant that the villainous teams' actions were portrayed in a realm basically separated from the rest of the game or the locations, etc., there, and as such just come off as a bunch of dramatic episodes detached from the rest or which aren't 'believable.' They hence mostly come across as
loud. This is part of why they would have to be followed all the time by 'allies,' to remind you that this is somehow a villainous team, or criminals, when otherwise they don't seem that related to the people or region of the game. Team Magma's 'ideals' don't come across as that affecting because they are merely abstract, TR strike people because they are in conflict with things. If TR didn't have any particular
ideals, then they would just turn themselves in.
The other aspect of this is that the teams became more a question of plot than their place in the game and region, so that while TR had an aesthetic, complemented by appropriate Pokémon, involving sneakiness, undermining normal order, undermining property rights (hence money), etc., the later teams are mostly reducible to just plot-specific goals such as awakening Groudon, etc., somewhat like the 'villain' in M02, and the rest mostly just follows from that. While TR obviously helped the franchise grow in some ways, after Magma it wasn't really any different.
It might not be as open as other main-series Pokemon games, but there was a little leeway in the order of battling Gyms and what you could do.
To be fair, while G/S became
very open, the later games were based on a conception of plot-based games à la Final Fantasy where this was railroading and either lacked or actively discouraged openness in the game, and hence came to lean on the gyms and conventional aspects perhaps a bit more than the early games, which could be more cynical and detached. The opening of D/P, for instance, is an example of them wanting a plot or progression and forcing a player into it to a degree which pretty much immediately violates the nature of the game itself and the relation implied in creating a 'player-character.' It must be noted, pleasantly, that while such plots may occur at times in other games with real cutscenes at that time, or movies, they were mostly not present previously in these games.
The disjunction in order, as in later games, followed a ghost-themed area.