This is a multi-issue problem that I have been dealing with since day one with Shopify due to the way it natively deals with products and variants. As a preface I work for a shoes store, and our shoes almost exclusively come in 40+ size/width combinations as well as multiple colors.
Problem one: the 100 variant limit. A significant number the "styles" of shoes we carry come in 4-5 widths and 13+ sizes, so it is impossible to include all of the color variants in one product. The problem with that is there is not easy way to show a customer all of the different color options on the product page for whichever color they may initially choose and to see them all they will have to search and/or navigate multiple pages. That seems extremely ineffective to me.
Problem two: With the "styles" of shoes that come in fewer size/width variants and I am able to include them into a single product page Shopify then treats them all as one color for the purposes of searches and collections thereby limiting the visibility of whichever color the customer may actually be looking for. Further when women shop for shoes sometimes the color is the primary factor and the style is secondary depending on the situation, so the inability to display all of the color variants is a significant limitation as well.
The solution that I'm ultimately looking for here is a way to Products that are all the same exact "Style" just different colors as Products for the purposes of collections and search, but then to treat them as Variants for the purposes of the product page.
I've already found the quasi-solution that displays variants as products in collections, but the limitation there is that it isn't selectively inclusive when trying to create a clearance collection, nor does it work with search or featured collection sections on the frontpage.
The most logical direction to me would be to separate each color within any given "style" into its own product, and find some way to toggle between the different colored products as if they were variants through the dropdown menu on the product page, but I haven't found anything close to resembling a solution there.
You can try Ultimate Product Filter+Search app https://apps.shopify.com/ultimate-search-and-filter-1 to display variants as separate products based on color options on both Collection and Search results page. It allows to search & filter by option, variant product meta fields. You can use metafields for variants to overcome the 100 variants limit in Shopify. They have a demo store https://usf-horizontal.myshopify.com/collections/shirts