If my invention has several innovative features, is it best to file separate patents for each feature, or for the device as a whole, or both?
I’ll start with a statistical answer. Each patent you file has a certain chance of being rejected, which can be a long drawn out process and you might give up. So if you file several patent applications in parallel, you are likelier to obtain at least one patent covering your system sooner. We often do this when we want to get a portfolio up fast - we file several patent applications, all with a request for expedited examination and hope to get 50% within a year.
There are practical considerations (other than money), as well. While you may have several innovative features, they may have many interdependencies. It may be difficult to capture these if you have separate patents. If you have a single specification and multiple claim sets, this means that a flaw in the specification can make the whole set of patents fall down.
There are scope considerations as well. If the ideas are independently innovative, you might want separate filings so you can explore and highlight how the different inventions are independent and have a scope broader than just the product.
There are litigation issues as well. Having multiple patents makes it more difficult for competitor to design around, more difficult for competitor to invalidate your patents and easier for you to choose the best patents/claims to sue on. Hopefully competitor will be so scared he will ask for a license. As a general rule, we assume that any give single patent will be invalidated or designed around.
Finally, putting budget aside, your goal is to obtain an granted independent claim for each of the innovative features and for the product as a whole and for various sub-combinations of features. I am assuming, by the way, that when you say “innovative” you actually mean “a patentable feature which is critical for my competition’s success” , since we file patents on what blocks competition, not (merely) on what is innovative. Note a competitor will often not copy your product as a whole but rather incorporate one or more of its features.
Of course, budget (and cash flow) cannot be put aside and the overarching question should be: what kind of protection can I both afford and answers my business needs.
For light bulb Edison's one patent was sufficient to prevent competitors from infringing his invention. But current day where knowledge is abundant and available at finger tips and due to the competition and case law created from numerous patent cases owning single patent would be risky. If Competitors are successful in circumventing the claim you are left with nothing to defend. My suggestion is file a single patent application but before grant file a continuation application or divisional application which would support you to add additional claims upon evaluation of the competitor product.