The Twins wouldn't have been a problem if the season had been Plot Centered, the Twins would have been forced into roles that served the plot instead of being able to hijack anything.
Because S2 was more character centered, new ill defined characters were allowed to take precedence over the plot. If the plot comes first, nothing can hijack it.
It all goes back to plot-centered. It's not mandatory for every show, but for an ensemble cast leading up to a major event (virus/explosion/whatever) Your choices are to go plot-centric or suck.
On other concerns... if the plot had been held up as a priority, then Adam, the villain, would have had to been more of a threat in order to make the plot work. As a character-centric season, 2 focused on certain characters at the cost of a plot-crucial character, Adam, and it obviously hurt the season.
Even the Malcolm Macdowell complaint. If Heroes had stuck with the plot-centricness, they could have retained the golden-child favor they had the first season and gotten someone truly awesome as, say, Maury Parkman.
For Peter's horrid storyline, that was born out of a need to keep Peter front and center. If the plot had been first, Peter would have been inserted in a well crafted plot where he best fit, making for an enjoyable storyline.
As for Season 1... if your complaint is a lack of special effects in the Finale... well... it doesn't sound like much of a failure... it sounds like 99% perfect.
Also, if you think it was the worst season final ever, then you need to go watch Smallville and compare. Then you need to watch the season finale to Season 2, where Peter has even more powers and MORE control and refuses to just walk through the wall and spends ten minutes ripping a big metal door off of its hinges, wasting time and energy, adding more holes to a character-serving ill conceived plot. If someone who likes the S1 finale has bad taste, then someone who likes the S2 finale has a bad memory.
As for character interaction... being isolated in plots no one cares about is only a problem if no one cares about the plots. Make a good story, and people will be interested. And I honestly think giving them their own plots that way was a way of trying to focus on the characters individually, instead of the plot and the relationships that energize it.