What you select for depends upon what traits are most important to you.

If all you do is save seed from all plants, selection still takes place naturally; plants which produce the most seeds per plant under your conditions will gradually become dominant. That is the reason that many gardeners see improvement year after year if they save their own seed.

When you intentionally select for certain traits, you may be inadvertently eliminating other desirable traits. Plants which bear more seeds per pod may - or may not - be more productive overall by weight. Same goes for seed size; there is often an inverse relationship between seed size & yield.

For some legumes (such as edamame soybeans) a higher number of seeds per pod is desirable. If your bean is used as snaps, more seeds per pod means longer pods, also desirable. If the bean will be shelled, however, the total yield per plant - regardless of the number of seeds per pod - should be considered.

Personally, if selecting at all, I would select for seed size before number of seeds per pod. All else being equal, larger seeds generally have a longer storage life.