You can still use the parents for the end game and Apotheosis just fine, it's just a matter of which characters you prefer more. If you are able to check out the Awakening Pairing thread it's geared towards Apotheosis optimization.
Part of the reason people don't like Donny is because he doesn't have a use for his lance rank (he's got two classes where he's stuck on E-rank weapons essentially taking longer to get decent and time and resources to train him up) and his bases are not that great (despite the fact that Donnel is apparently a better father for Apo than Kellam for some reason if you read through a few pages of the Pairing Thread). Plus villager is the weakest class in the game as I'm sure you're aware of. There is a reason I gave you the link to the max stat calculator too. It doesn't just have all stat mods for everyone it's a very useful resource (if I do say so myself) as it also has all of everyone's classes. Children included.
Let's just use Lucina as an example here because she's the obvious choice for reasons (read mother bias here because I adore my Little Angel...) if you haven't had a chance to check the calculator out to see how it works.
There are two columns (for the children) where you have a few choices the first is the "parent" column which has a list of all Lucina's potential mothers. The second one you have is the "classes" column which obviously lists classes but it also has Lucina's Modifiers. (Or the classes available to the "parent" characters as well as their modifiers)
E.g If Lucina has Robin selected in the "parent" column, then you will have in the "classes" column Lucina's "base classes" (essentially the ones that Chrom gives her): Lord, Cavalier, Archer and their promotions as well as the DLC Class Bride then Lucina's Stat Modifiers. All of the classes that her mother gives her are listed below the modifiers (or the selected "parent" if you will for the other children).
(ETA: Morgan is a special case as depending on the parent you chose will depend on the class that they're in when you recruit them. Morgan will only be a tactician when you recruit him/her if Chrom, Lucina, Walhart or Olivia is his/her parent as those four have classes that Morgan can't reclass into.)
Obviously for a first playthrough of Awakening I'd say just do what you want to do and have fun. Multi-runs are where you start trying to work out how to beat the game a bit better/seeing what other choices do etc.