Regex for capturing command flags and values

Instead of juggling around with quotes, take a far superior approach: use a conditional regex.
The basic form is as follows:

(?(1)foo|bar)
# Meaning: if group1 is set, use foo, otherwise bar as subpattern

For your requirements, this comes down to:

--(?P<key>\w+)=(")?(?P<value>(?(2)[^"]+|[^\s]+))

In PHP code and with explanation, this looks even more beautiful:

<?php
$string = 'helloworld --name=stretch --message="Hi there everyone"';
$regex = '~
            --(?P<key>\w+)=         # look for two dashes, capture every word character into the group "key"
            (")?                    # look for double quotes and make the group (2) optional
            (?P<value>              # save the following to the group "value"
                (?(2)[^"]+|[^\s]+)  # if (2) is set, capture everything BUT a double quote
                                    # else capture everything but a space (not allowed without quotes)
            )
            ~x';                    # verbose modifier
preg_match_all($regex, $string, $matches, PREG_SET_ORDER);
foreach ($matches as $match)
    echo "Key: {$match['key']}, Value: {$match['value']}\n";
/* output:
Key: name, Value: stretch
Key: message, Value: Hi there everyone
*/    
?>

See a demo for this one on ideone.com.

You can even go further and allow single quotes as delimiter and have escaped quotes in your values like so:

--(?P<key>\w+)= 
(['"])?                   # allow single or double quotes
(?P<value>       
    (?(2).+?(?<!\\)(?=\2) # if (2) is set, match everything lazily afterwards
                          # and make sure that what follows is the formerly captured quote
                          # make also sure that what precedes, is not a backslash (thus allowing escaped quotes)
    |[^\s]+)
)

See this demo on regex101.com (hijacked from @SebastianProske, sorry mate :).