It's fairly common for the design of featural conscript glyphs to be at least partly informed by the manner of articulation and/or place of articulation, but you could also consider:
Articulatory phonetic information – glyph-level
* Place in the sonority hierarchy, or, roughly, the amplitude
(For all examples I will assume a horizontal script comparable to English.)
Position in the sonority scale could be represented by increasing lengths of ascenders or descenders, potentially giving every written word a silhouette that follows a low-high-low, low-high, high-low, or high-low-high pattern.
* Length or gemination
A doubled or tripled ligature, an elongated horizontal stroke, or tick diacritics, could indicate when a consonant should be geminated; the number or length could indicate how long it should be held, if multiple lengths are possible
Pronunciation cues – syllable-/intersyllable- or word-level
* Tone
In tone-marking scripts (Thai, Chinese Zhuyin and Pinyin, others), a diacritic indicates whether it's a falling, high, mid, rising, or low tone. In some scripts no diacritic indicates no tone, and in others it means a default tone. Tone changes the pronunciation and meaning of a syllable/word, as seen in this example:
* Emphasis or lexical stress
In accordance with your conlang's stress patterns, a stressed syllable could be indicated by an alternate form of the nucleus (generally a vowel), or a diacritic applied to the vowel or the entire syllable. Changing the stress can, as in the English examples of conduct and conduct, differentiate a noun from a verb, or highlight the important part of a sentence (as in "are we going?" versus "are we going?" versus "are we going?").
* Hiatus or diaeresis of vowels
Hiatus is a slight pause that occurs when a coda-less syllable abuts the nucleus of the next (as in co-operate); this would only need to be indicated if your languages uses diphthongs (two or more vowel glyphs written in sequence), which isn't exactly featural (though Hangul does it). It might also be useful if your script does not use spaces (as in many eastern Asian scripts) or linkages (as in Devanagari) to define a word space – hiatus would indicate the start of a new word when the preceding word ends with the same vowel and would produce an unintended third word if the pause is omitted.
* Intervocalic transformation of consonants
Indicating whether or not an intervocalic consonant should undergo lenition could indicate the pronunciation pattern a word should follow. 312
For example, intervocalic t → d (bottle → "boddle") may not change the meaning of the word, but could convey the social context or significance of the speaker or subject (e.g. "boddle" might be slang and carry additional connotations).
* If your language uses vowel harmony or metaphony, diacritics could indicate the scheme to be applied to given vowels
If your language classifies vowels into classes (as <PERSON> does) there may be rules that determine which vowels can go together in a word, or in which order they must go. If you have well-established patterns vowels follow, a diacritic may indicate following vowels should be pronounced a particular way (the equivalent of other vowel glyphs, but their use conveys a particular meaning), or that a vowel is exempt from these rules (as it is a loanword, for example).
Structure or parsing – word- or sentence-level
* Prosodic stress
Prosody can be similar to stress as mentioned above, but operates at a multi-word level to indicate things like sarcasm, focus, type, etc. Specific glyphs such as a mark between words or under/over-lines, could indicate where entire words or clauses should be stressed, how long to pause between them, if cadence should be applied, or if a particular phrase should be understood as an idiom. In English, prosody tells you if a spoken sentence is a question, and the question mark represents the sound change in the final syllable. 312