No he hasnt missed that many games, but the point still stands. Fast bowlers simply dont have the same kind of fitness records as batsmen and its pointless to have a player as captain if the Vice captain is going to have to take over many a time.
As far as who are the replacements are, a quick glance at the domestic competition tables would suggest that any of Jos Buttler, James Hildreth,Jimmy Adams, Craig Kieswetter, James Taylor, David Payne and George Dockrell could step in as replacements. Its easy to sit down and take the conservative route and say that there are no replacements, there are no replacements only when no one is given a chance. Players like Bell and Bopara have been given 2 world cups and have been dismal failures for both of them. To give them another is really disrespecting the point of having a domestic cricket system in place.
AFAIC, looking at a future squad, the nucleus of the bowling would still be the same. Bresnan, Broad, Anderson, Swann, Shahzad isnt a bad lineup at all. Throw in Onions, Dockrell/Rashid and perhaps Woakes and someone else young like Payne and there is enough potential there. The batting is what needs drastic changes but the likes of Trott and Morgan provide enough stability to be able to bring changes around.