If a hosting provider restriction is causing you to consider a Joomla multi-site solution, then it may be easier to find an alternative host and build the websites individually than complicating things with a Joomla multi-site which will inevitably involve some compromises.
Most shared hosting accounts can be configured to host more than one Joomla website either by creating multiple databases or by using different table prefixes in the same database.
Multi-site vs Individual Sites
Obviously there are pros and cons to building separate websites compared to combining them into one Joomla install. You need to think carefully about whether a multi-site solution will work for the particular scenario and you may need to make some compromises.
It is more difficult to set up a multi-site website initially but less ongoing maintenance is required as you only need to apply Joomla and third party updates and run backups etc on one website.
If something breaks on a multi-site solution, you may lose all the websites rather than just one website.
Note that not all third party extensions work as intended on a multi-site solution.
Official Multi-site Solution Not Recommended
The official instructions at Multiple Domains and Web Sites in a single Joomla! installation direct you to edit the template
index.php file. This is not considered best practice as template updates can overwrite your changes in future.
Third Party Multi-site Extension
It is probably better to use a third party extension such as the free Virtual Domains or similar which avoids hacking the core code.
Note: The remainder of this answer is written from limited experience with one implementation of Virtual Domains. The items listed may or may not be relevant to other third party multi-site extensions or even Virtual Domains configured in a different way.
Create separate content categories for each website (this is important for search).
Modules aren't so easy to categorise as some modules may be common to all websites. You could use the Joomla 3.x "Note" feature to help keep track of which modules apply to which websites.
Will the individual websites have their own look and feel? If so, it is probably easiest to install a different template for each website.
Virtual Domains enables you to specify a different template for each website.
Will the individual websites have their own menus or share a common menu?
Using RocketTheme Gantry 4 templates I found it was easier to set up one menu and use the "Menu Filtering" feature in Virtual Domains to specify which menu options applied to each website.
Virtual Domains enables you to specify a home menu item for each website.
Assuming search results should be limited to the website that is being searched, enable Smart Search and create a filter for each website at Components -> Smart Search -> Search Filters by selecting appropriate categories for each website.
You can then create a Smart Search module for each website using the appropriate filter you have created for each website. Set up the Menu Assignment in each search module so the modules are displayed on the appropriate pages on each website.
Multi-site Global Configuration Items
Ideally, the multi-site extension you choose should let you specify unique Global Configuration items for each website.
Virtual Domains lets you specify a unique Site Name, From Email, From Name, Meta Description and Meta Keywords for each website.
Multi-site Search Engine Friendly Urls
With SEF enabled, each page requires a unique url across all the websites. For example, if I have two websites in the multi-site website, www.acmeproducts.com and www.acmeservices.com, then they can't both have about us pages like this:
The urls need to be unique so the about us pages will need to be more specific like this or similar:
Multi-site User Accounts
By default, registered users on one website will be registered users on all the websites which may or may not be an issue.
Hopefully this gives some idea of what needs to be considered before being able to decide if a multi-site solution is appropriate for the particular scenario.