Its not really case by case. No indie title can match or has matched the production value of a major publisher/developer, I mean that's just basics of logistics. They can make great, beautiful games but then, conversely, they will be short or very light on asset uniqueness.
Pushmo/Crashmo have the same breadth of content as indies if not more-so, with a whole community of shareable levels. Toad is a ways above Pushmo in production value and required dev time even if it uses the same 3DWorld engine. To say that Toad is priced at a higher premium than a 2D puzzle game or any 2D puzzle/indie game shouldn't be revelatory or strange as its production costs and complexity are considerably higher. Moveover, Toad is designed in full 3D perspective gameplay, not 2D on 3D or just 2D. The level of development to a singular level increases substantially when change from 2D to 3D and even more from 3D to literally any dimension of three dimensional space.
A game can be busier on the basic impressions, as per your example of other Frozen Byte games, doesn't mean it was harder to create. The more axis you add to a free-rotating game, the more time consuming it becomes to create because you have to spend time planning a truly 3D dimensional object presented in 2.5D, whereas most games create objects that you will only see in certain forms/fronts/aspects in fixed 2.5D vision with a possibly moving camera, but still fixed around a central and unitary axis.