you can do it through code:

as an example:

    SPList list = web.Lists["My List"];
    list.EnableVersioning = true;

so the above can be simply added to your code when your creating the list:

somthing on the lines of:
    
    //get web object from context
    SPWeb web = SPContext.Current.Web;
    //get list collection
    SPListCollection lists = Web.Lists;
    //add list to list collection
    lists.Add("My List", "My list for user input form", SPListTemplateType.GenericList);
    //call list that we just made
    SPList newMyList = Web.Lists["My List"];
    //enable versioning on that list
    newMyList.EnableVersioning = true;


http://msdn.microsoft.com/en-us/library/microsoft.sharepoint.splist.enableversioning.aspx

**EDIT**

i get you! when adding the list using vs2012 you can go into the xml of the list (Elements.xml ):

    <ListInstance 
      CustomSchema = string
      Description = "Text"
      DocumentTemplate = integer
      FeatureId = "Text"
      Hidden = "TRUE" | "FALSE"
      HyperlinkBaseUrl = string
      Id = Text
      OnQuickLaunch = "TRUE" | "FALSE"
      QuickLaunchUrl = "Text"
      RootWebOnly = "TRUE" | "FALSE"
      TemplateType = Integer
      Title = "Text"
      Url = "Text"
      VersioningEnabled = "TRUE" | "FALSE"
    </ListInstance>

the above is appended within the list elements.xml as you can see within ListInstance you have VersioningEnabled, just add that like so: VersioningEnabled = true and versioning is enabled to that custom list.

for major and minor versions that is the same concept here again:

http://msdn.microsoft.com/en-us/library/office/ms415091.aspx

    <List
      BaseType = "Integer" | "Text"
      Default = "TRUE" | "FALSE"
      DefaultItemOpen = "Integer"
      Description = "Text"
      Direction = "Text"
      DisableAttachments = "TRUE" | "FALSE"
      DraftVersionVisibility = "Integer"
      EnableContentTypes = "TRUE" | "FALSE"  EnableMinorVersions = "TRUE" | "FALSE"  EnableThumbnails = "TRUE" | "FALSE"
      EventSinkAssembly = "Text"
      EventSinkClass = "Text"
      EventSinkData = "Text"
      FolderCreation = "TRUE" | "FALSE"
      Id = "GUID"
      ModeratedList = "TRUE" | "FALSE"
      ModerationType = "TRUE" | "FALSE"
      Name = "Text"
      OrderedList = "TRUE" | "FALSE"
      PrivateList = "TRUE" | "FALSE"
      QuickLaunchUrl = "URL"
      RootWebOnly = "TRUE" | "FALSE"
      ThumbnailSize = "Integer"
      Title = "Text"
      Type = "Integer"
      Url = "URL"
      URLEncode = "TRUE" | "FALSE"
      VersioningEnabled = "TRUE" | "FALSE" 
      WebImageHeight = "Integer"
      WebImageWidth = "Integer">
    </List>

you append the above within the schema.xml that belongs to the list with the elements.xml

http://msdn.microsoft.com/en-us/library/office/ms459356.aspx