Proper timing for submitting a paper Is there any general advise on when better to submit a paper?  

I mean, should one consider the seasonal differences in the way journals work.  

Let's say, I have a manuscript ready to submit at the beginning of June. Would it make any sense to withhold it until the beginning of the new academic year as there is low chance the paper would be proceeded during the summer?
You should submit it once you finished. You should not wait or think about for new academic year. This is your misconception to have less chance to publish in summer. Because all the manuscripts goes under review process which takes usually 2-3 months and then it will be decided for next step.