There are several factors to consider, some of which suggest wives which will be suggested against by other factors.
Its really a matter of what matters most to you.
1. # of Avatar/MU Children vs. Morgan's stats
Marrying 1st gen grants an extra child; you have Morgan and her sibling. This grants the sibling an Avatar/MU-like class set (access to all regular classes of their gender + Tactician/Grandmaster). This will make them very powerful, more so than if they had another father in most cases.
However, marrying a 2nd gen wife means that Morgan will have marginally higher stat caps. Generally it will only be 1-3 points higher in absolute total modifiers. However, if you pair up the wife's parents to breed her for a particular stat at the expense of another and then you set up your Avatar to be strong and weak in the same stats then you can get a really high value in a stat that is very important to you at a cost of a really low value in a stat that isn't as important to you.
This can make your Morgan extremely powerful at the area of specialization, but sacrifices the opportunity to make one of the other kids a super MU-like unit as well.
2. Skill distributions for the children (often focused around Galeforce)
Kjelle, Noire, and Nah can only get Galeforce if their fathers are Donnel, Gaius, or the Avatar.
If you insist that every character who can possibly have this skill get it then you would have to marry the Avatar to one of Sully, Tharja, or Nowi and then marry Donnel and Gaius to the other two.
If you're okay with one of these girls not getting Galeforce (for example, if you're not planning on using one of them because there are too many characters to practically use or if you've already arranged for more than enough Galeforce users to suit your purposes), then there is no need to have the Avatar marry any of their mothers.
3. Effectiveness of the wife as a partner in combat
From the standpoint of fighting together in a pair-up its best that your wife has a good skillset orientated for combat. This basically means Galeforce, a damage-increasing activation/proc skill, and a good selection of quality combat classes.
Generally speaking the most effective wives as combat partners will either be 2nd generation wives or a handful of 1st generation units (particularly Sumia, Cordelia, or
) who qualify for the above conditions.
Often the degree to which a child benefits from getting skills they "needed" from the Avatar is inversely related to the combat quality of the wife.
2nd gen wives don't have children of their own (only Morgan from the Avatar), so their children don't benefit at all, but 2nd gen wives tend to be the best at combat.
Likewise, the best 1st gen combat wives with children of their own, Sumia and Cordelia, have kids who will always turn out amazing pretty much regardless who parents them because Sumia and Cordelia already have amazing skill and class sets.
And then you have Sully, Tharja, and Nowi, whose kids have a lot to gain from Avatar parentage but whom themselves end up holding the Avatar back in combat, as they tie his S-rank to a Galeforce-less unit (and he cannot get the skill himself either). In Nowi's case she's also lacking any useful damage increasing activation skills.
4. Then there is if the wife actually wants the Avatar as a husband.
For example, with her 100% dual strike rate Lucina might be better served with a Galeforce husband so she can leverage this three times a turn, rather than twice with the Avatar.
5. Special skills the wife can give Morgan
Lucina gives Aether and
gives Shadowgift. However, Luna/Ignis is more practical than Aether for certain reasons and Shadowgift is often a waste in which you'd be better off going as a Sorcerer anyways.