I have decided to go for ILR on the basis of 10 years and then apply for my wife on FLR(M). And using salary from limited company as source of earning
Join income can be used for FLR(M) and cannot be less than £18,600pa. You will also need to submit SA302 etc for self employment and make sure your tax affairs are in order. 12 months of your financial records for self employment and she can use 6 months of payslips and bank statements.
Your wife will have to wait 5 years on FLR(M) - 2 x 2.5 year FLR(M) visas - before she qualifies for ILR. She cannot count time already spent as PBS Dep towards this requirement.
You will also have to pay the immigration health surcharge of £500 before submitting her FLR(M) application, this is on top of the visa application fee (£649 by post or £1049 in person).
She needs English level A1 for FLR(M) application from an approved HO test provider.
2 years proof of cohabitation for subsisting marriage required.
Tier 1 route to ILR for you and dependent is still the better and cheaper option long term, but it is your choice.
Remember that even if you apply on 10 years basis, HO still checks tax paid to HMRC, income declared to HO/HMRC etc.