Another benefit of merging is being able to track a hybrid mobile experience, where the user starts out in your app, is linked from the app to web content and then returns to the mobile app. Currently, two report suites will not allow you to follow the user's flow from one to the other.
(Image credit: Adobe Consulting)
As long as you have implemented them in a similar way, it will be a lot easier. Just make sure you have an eVar that identifies which environment the tracking calls are coming from. Another thing to keep in mind is handling historical data. If you decide to merge one report suite into the other, whichever suite you end up choosing, you will need to make sure it is formatted as a Mobile report suite, plus, you will want to run in parallel with the other existing suite for 13 months so you can capture year over year, then drop the other report suite.
If you end up moving both web and mobile into a brand new report suite, you will have to fire secondary calls in order to maintain a year's worth of data for both original report suites until you have enough historical data (again, 13 months). Or, if you're not worried about historical data, you can skip that step.
The points above about creating virtual report suites are valid and can be useful to you if the business asks for it.
It would be great if you can have a global report suite associate to capture both the data. Once you create single report suite for both the instance you can use multiple "Virtual Report Suite" based on the requirement by applying the segments to differentiate the website and mobile and other sub-directories.
If you create multiple report suite for account, please remember you can use up to "1000" report suite per account and that too will not delete the report suite once created.