A sane alphabet. Cyrillic before the 20th century had some freaky things and weird use of letters that we still have. Aficionados say that ‘ѣ’ and ‘ъ’ could be properly used only by people who memorized all the words with them. (Which is not how modern Slavic languages work, even though English-speakers wouldn't bat an eye at that inconvenience, hur hur.)
In Czech, some "y" vs. "i" can't be deduced. Schoolchildren need to drill the words that use "y". Similarly to what "ѣ" had with бѣдный блѣдный бѣлый бѣсъ, except our thing doesn't even rhyme :)
(Not that I'm complaining. As you note, English is vastly worse in this regard.)
My knowledge here is limited, but I have noticed that some language families tend to get simplified over time versus their common ancestor. For example, Italian and French (and all other Romance languages, I believe) have lost Latin's case system and all the memorization that entails. Italian is much easier to learn than Latin in my experience. So if the same is true for the common ancestor of the Slavic languages, you would be learning a much more complicated language than any of the current Slavic ones.
I (a non-Slavic language speaker) would imagine the divergence between the modern Slavic languages would be dwarfed by the divergence between those languages and Proto-Slavic or Old Church Slavonic.
Quite the opposite, I believe. My native tongue is Polish (West Slavic) and I speak decent Russian (East Slavic) as a foreign language. My subjective feeling is that there's more in common between either of those languages and OCS than between the two directly.