Their rarity will stay as is, non-ms or ms active.
And as said by Tatsu, Bagons are now only to be found at Meteor Falls B1f 2r(M/D/N), Hoenn. While, Larvitars can only be found at Kanto.
There are numerous things, few of them are:
*Catch all MS exclusive pokes atleast 1 each just to expand your pokedex seen&caught data. ex. Axew, Clauncher, Skrelp, Alomomola, etc.
*Avail the Doctor quest finish it as soon as possible, for if youre MS active u can easily get into max tier. Check the Doctor quest guide.
*The Aerodactyl quest at Leev town(MS exclusive area).
*The Sevii Islands Quest(MS exlusive area).