Hey Berries,
Starting to fall in love with all the very classic names at this point and am now considering [name_m]Jonathan[/name_m] for the list. My grandpa is [name_m]John[/name_m] so in a sense it could honour him. I really love the overall sound and that he could go by [name_m]John[/name_m] or [name_m]Johnny[/name_m] as I am a major nickname person (and really like [name_m]Johnny[/name_m] too.) Funnily enough I even met a [name_m]Jonathon[/name_m] the other night!
Thoughts please! 
There is nothing wrong with [name_m]Jonathan[/name_m] but it does feel a little dated and not as classic as [name_m]John[/name_m]. I would prefer [name_m]John[/name_m].
It’s funny, considering that [name_m]Jonathan[/name_m] is a biblical name it doesn’t have the love and popularity of the more trendy biblical names, like [name_u]Noah[/name_u] and (at least on nameberry) [name_m]Ezra[/name_m]. I like the rhythm of it, and it certainly lends well to the nicknames you’ve mentioned. It doesn’t make me swoon, though.
[name_m]Jonathan[/name_m] is a great name with multiple nicknames. I think is a nice way to honor your granfather. I like the nickname [name_m]Johnny[/name_m], but spelling [name_m]Jonny[/name_m] or [name_u]Jonnie[/name_u] because [name_m]Jonathan[/name_m] spelling.
[name_m]Jonathan[/name_m] is a solid, underused choice.
I think [name_m]Jonathan[/name_m] is very handsome. [name_m]John[/name_m] + [name_m]Nathan[/name_m], what’s not to like?
I definitely prefer this spelling to [name_m]Jonathon[/name_m] or [name_m]Johnathan[/name_m].