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Yes this does seem to be a bit of an issue for your wife. The fact is that she does have leave to remain in the UK on a settlement visa which is issued for 30 months, now during those 30 months she would not breach her visa conditions if she was to remain outside of the UK for longer than the 90 days indicated.
In respect of your first concern, yes if you continue using the visa for a spouse and are not present in the UK the home office would prefer it if you informed that this visa is not appropriate and you would require a different type of visa. Now in terms of applying for further leave to remain, there is no requirement that you would have to be in the UK for 90 days prior to applying for an extension, but as you correctly mentioned if you have not used the visa for the purpose it was issued for ie settlement then the home office will get suspicious and may question you intent, but would not be a strong grounds of refusal provided that sufficient evidence ie business, family health can be provided for her having to travel outside of the UK.
The only visa she would be able to apply for is a visit visa which would be granted for 6 months and thereafter she would need to apply again every time she enters the UK it would basically be everything you have mentioned in your question and would not be ideal in your situation.
Should she wish to travel in and out of the UK on a spouse visa, although it is not necessarily a breach of her visa conditions, what it may mean is that next time she applies for an extension the home office may scrutinise the application/applicant's intention more. The fact is that if she does abuse this visa then , it would be difficult for her to obtain further leave to remain (but not impossible), but if she switches to a different visa it would definitely be a case of applying every time she wishes to enter the UK.
If over the 60 months she does not meet the residential requirements to apply for indefinite leave to remain then what this would mean is that she would need to keep on applying for further leave to remain until she is able to meet the requirements for indefinite leave to remain. The home office will not grant indefinite leave to remain to individuals whom cannot demonstrate an intention to remain and settle in the UK indefinitely.
I hope the information given above helps you to make up your own mind as to what the best route for you to follow is. I know this is a a lot of information to take in and I would be happy to clarify and issues with you. I hope this answers your question, if so kindly rate my answer positively. If however, you feel that the answer does not cover all the points raised in your question, please DO NOT rate my answer negatively, I will be happy to answer further question until you are satisfied with my answer.