I'll start by correcting your question:
"Why is 'says' different from the others?"
Remember the word order for questions: the verb (is) has to come before the subject ('says').
We can't say 'different of...'. The standard collocation is 'different from ..'.
And the answers:
1. It just is. /sɛz/is the standard pronunciation, although people in some regions may say /seɪz/, depending on their local accent.
It's something that happens over time, especially with very commonly used words. Often a pronunciation variant from one region becomes mainstream with one word but not with others. (This also accounts for many of our irregularities in spelling, by the way) One thing we do know is that this change isn't new: there's documentary evidence that people said /sɛz/ hundreds of years ago.
2. Well, don't forget that the past tense follows suit.
The only other word I can think of off-hand is the past simple 'ate', which can be pronounced either /eɪt/ or /ɛt/. The /ɛt/ variant was the standard correct pronunciation in Britain for a long time, and it is still used by many older and/or posher people in England. Younger Britons are more likely to say /eɪt/ these days.
There's also the interesting situation where older versions of English, still seen as correct in the UK, have survived only in country areas of the USA and so are looked down by most Americans. If you ask any American how to say 'ate', they'll say that the proper pronunciation the same as the number 8, and that anyone who says 'ett' is probably an ill-educated southerner. The same goes for the past tense 'learnt' - correct in BrE but disparaged in the US.