The question of there being a 'best' version of Sensible Soccer (or SWOS) is a separate matter to that of a specific team or player being better or worse in any particular version.
For each update, players and teams were revaluated in real life by researchers, with the relative skills and weaknesses of their SWOS counterparts being based thereon. The focus of research seems to have been on the main footballing nations, and so players in less prominent leagues tend to be generalised somewhat.
Fluctuations in players' abilities and careers are on the whole accurately reflected, as is the overall strength of sides, whether club or national. So if you want to play as Everton at their strongest, 1996/97 is probably the edition.
The major difference between Sensible Soccer and SWOS is the expansion of the management element. In SWOS, one can play a 20 year career game, wherein one can buy and sell players, switch clubs, and even progress to national management and pick a squad. There is an option to purely manage matches, in place of actually playing them.
A noticeable, but subtle, global change between different editions is in the gameplay during matches, regardless of the team controlled. A basic guideline is that the later the edition, the slicker the play. Player ball control is generally better, passing is more flexible, the computer controls outfield players more intelligently, etc. That is not to say that the first Sensi Soccer plays badly; just differently. I recommend trying a few versions for yourself and deciding which you prefer.
Only ever played Kick Off 2 once myself. Didn't like it.