This can be done by using custom tags, that includes all parents, and hand-picked clones.
The problem is, how do you add tags to only parents?
There are two ways of doing this. Both methods have their disadvantages, so choose wisely!
Method 1 : Elegant, but requires MS-Office
#1. Open MS Excel.
#2. Copy contents of romlist file into sheet
#3. Data->Text to columns (this may differ from Office version, though)
#4. A wizard will appear. Set delimiter to ';' (Am's delimiter). Set all column to 'text' type (few games may affected by this)
#5. If done correctly, the romlist will be nicely analyzed into columns
#6. Add 'filter' to each columns
#7. Choose 'CloneOf' column, and select 'empty' entry only. (only parent roms will be shown)
#8. Copy the contents of '#Name' column into a new text file.
#9. Save the text file. this file is tag file (containing only parent roms)
#10. The name of tag file created in #9 acts as tag name in FE. Copy the tag file into appropriate romlist directory
Method 2 : (very) hackish method. But works anyway
#1. Backup the favourite file for the mame list, and delete it.
#2. Create a temporary layout, as follows
list temporary
layout basic
romlist mame
filter parent_not_favourite
rule CloneOf not_equals .+"
rule Favourite equals 0
filter verify_parent_favourite
rule CloneOf not_equals .+"
rule Favourite equals 0
filter verify_no_parent_favourite
rule CloneOf equals .+"
rule Favourite equals 1
(you may have to modify "romlist mame" to your list name, if not mame)
(actually, only first filter is used, second/third is for verifying purpose)
#3. Launch AM, switch to above temporary list and first filter
#4. Mash 'add to favorite' button repeatedly. You may want to set AM's option 'confirm favorites' to 'No' temporarily...
#5. It would take about 2000~3000 strokes to finish. Once finished, first filter should be empty.
#6. (surprisingly) Now all parent roms are marked as 'favourites'. Close AM.
#7. Copy the favorites to tag file.
Favorites are stored in <AM Directory>/romlists/<romlist name>.tag
Tags are stored in <AM Directory>/romlists/<romlist name>/<tagname>.tag
#8. Restore original favorites file in #1, if necessary
Once either Method 1 or 2 is done, all parents will be marked as some_tag.
Then you can add clones of your choice by also marking it as some_tag.
Lastly, initial filtering rule
rule CloneOf not_equals .+"
can now be replaced as
rule Tags contains some_tag