One thing I really want from PokeSpe is a break from all the plot and seeing the daily lives of the characters, the 'dexholders especially, and daily interactions with the others. Like Platinum fan stated, seeing scenes like the girls having a day to themselves or mundane stuff like that would be a great welcome. (Naturally, I don't want any romance subplots, just good old friendship.)
The older 'dexholders need this more than the newer, really. I want to see the characters being themselves rather than being the heroes. Some of them are kids, after all. Plus, I'm insanely curious as to what teenagers do in the Pokemon world.
If Sakaki has simply told us that he has tried other methods or if we had flashbacks along with more clarity on the purpose of Deoxys, it would of worked better. The manga never attempts to make us believe that Silver was what TR was always after or that Deoxys was last option left. Since the writing never attempts to do any of that is why I feel like it doesn't make sense nor works.
The whole thing with "Deoxys is for Silver" was poorly thought out. Good idea, bad execution.