A sequel doesn't have to take place immediately after it's predecessor, nor does it need to have the same characters. As long as it takes place along the same timeline, and after the game preceding it, it qualifies as a sequel. Spinoff =/= sequel. For some more proof, have this.
se·quel /ˈsikwəl/
–noun
1.
a literary work, movie, etc., that is complete in itself but continues the narrative of a preceding work.
spin-off /ˈspɪnˌɔf, -ˌɒf/
–noun
any product that is an adaption, outgrowth, or development of another similar product.
With those two definitions, keep this in mind. In order for a sequel to be a sequel, it only needs to be along the same timeline and keep in the same universe. A spinoff needs to be either concurrent to or immediately following the original product,There are similarities, but by no mean are they the same. Yes, the Mega Man series does share characters, but since they aren't concurrent or immediately after each other, they aren't spinoffs. With the exception of the Battle Network/Star Force timeline which IS a spinoff, the rest of the games are along the same timeline. And therefore they are sequels to the preceding series.
In short, since all the series can be self-contained yet continue the narratives of the preceding series (with the exception of BN->SF), they are sequels. They are not spinoffs, since spinoffs are not self-contained.