Nintendo's current digital valuation of those games on the Wii U are £9 for Mario 64 and £18 for Galaxy. We could reasonably price Sunshine in the middle at £13.50.
If the plan is to sell digital games separately for those systems' catalogues next year, then the total cost of those games would likely be around £40.50, compared to the £50 RRP and digital price of the 3D collection. Bundling those games physically and especially digitally in the meantime could therefore actually lead to more revenue up to then.
Once the games are available separately then the digital bundle becomes obsolete, at least at that price, hence the limited availability. The digital bundle would be even more obsolete if N64 games, including Super Mario 64, are added to the online service and you only had to purchase the other two separately.