TL;DR & the actual question
For those who don't need an explanation of all verb endings and the ways in which they differ from each other, my question follows below. For those who might need a refresher or explanation, jump to "The indicative present system" heading.
Why, when compared to the perfect system and its extremely regular endings for each tense between conjugations (i.e, 1st, 2nd, etc.), are the present system and its endings for each tense so dissimilar between conjugations?
Is it a result of some change verbs underwent while evolving from Proto-Italic predecessors of Latin? Is it an artifact which arose due to the way(s) by which Proto-Indo-European verbs worked? Or is it something else?
Irregular verbs are, obviously, exempt from this.
The indicative present system
In the Latin present system (present, imperfect, and future tenses), verb endings for each tense in each conjugation differ from each other quite a bit. In the present indicative (active and passive), 1st, 2nd, and 4th conjugation verbs largely retain the vowel present in their infinitive:
- 1st: -ō/-or, -ās/-āris, -at/-ātur, -āmus/-āmur, -ātis/-āminī, -ant/-antur
- 2nd: -eō/-eor, -ēs/-ēris, -et/-ētur, -ēmus/-ēmur, -ētis/-ēminī, -ent/-entur
- 4th: -iō/-ior, -īs/-īris, -it/-ītur, -īmus/-īmur, -ītis/-īminī, -iunt/-iuntur
Whereas in the 3rd and 3rd-io present indicative conjugations, the vowels in their infinitives are not retained at all:
- 3rd: -ō/-or, -is/-eris, -it/-itur, -imus/-imur, -itis/iminī, -unt/-untur
- 3rd-io: -iō/-ior, -is/-eris, -it/-itur, -imus/-imur, -itis/-iminī, -iunt/-iuntur.
The imperfect indicative tense (active and passive) is slightly more regular, as the endings of all conjugations will ultimately terminate with -bam/-bar, -bās/-bāris, -bat/-bātur, -bāmus/-bāmur, -bātis/-bāminī, and -bant/-bantur. However, even with slightly more regularity, each conjugation will still insert a certain thematic vowel or vowels between the present stem and imperfect endings, those being:
- 1st: -ā-
- 2nd & 3rd: -ē-
- 3rd-io & 4th: -iē-
Which ultimately results in verb endings which differ between the conjugations.
In the future indicative tense (active and passive), while being somewhat more regular than the present, verb endings once again vary between conjugations. In the 1st and 2nd conjugations, the future endings are almost identical to each other with the only difference being the vowel retained from the infinitive:
- 1st: -ābō/-ābor, -ābis/-āberis, -ābit/-ābitur, -ābimus/-ābimur, -ābitis/-ābiminī, -ābunt/-ābuntur
- 2nd: -ēbō/-ēbor, -ēbis/-ēberis, -ēbit/-ēbitur, -ēbimus/-ēbimur, -ēbitis/-ēbiminī, -ēbunt/-ēbuntur
Whereas in the 3rd, 3rd-io, and 4th conjugations the future indicative endings are completely different from those of the 1st and 2nd conjugations and contain no vowels retained from the infinitive:
- 3rd: -am/-ar, -ēs/-ēris, -et/-ētur, -ēmus/-ēmur, -ētis/-ēminī -ent/-entur
- 3rd-io & 4th: -iam/-iar, -iēs/-iēris, -iet/-iētur, -iēmus/-iēmur, -iētis/-iēminī -ient/-ientur
The subjunctive present system
When it comes to the subjunctive present system, more regularity can generally be found than what would be found in the indicative.
For the subjunctive present tense (active and passive), the endings of all conjugations (except for 1st) will always end with -am/-ar, -ās/-āris, -at/-ātur, -āmus/-āmur, -ātis/-āminī, and -ant/-antur. Thematic vowels will then be inserted between the present stem and present endings for the 2nd, 3rd-io, and 4th conjugations, those being:
- 2nd: -e-
- 3rd-io & 4th: -i-
In the 3rd conjugation, the previously stated endings are used without a thematic vowel. In the 1st conjugation, the endings -em/-er, -ēs/-ēris, -et/-ētur, -ēmus/-ēmur, -ētis/-ēminī, and -ent/-entur are used instead.
The subjunctive imperfect (active and passive) is much like the indicative imperfect. The endings for each conjugation will always terminate with -rem/-rer, -rēs/-rēris, -ret/-rētur, -rēmus/-rēmur, -rētis/-rēminī, and -rent/-rentur. However, like the indicative imperfect, each conjugation will insert a certain thematic vowel or vowels between the present stem and the imperfect endings, those being:
- 1st: -ā-
- 2nd: -ē-
- 3rd & 3rd-io: -e-
- 4th: -ī-
Which once again, like the indicative imperfect, results in verb endings which differ between conjugations.
The indicative & subjunctive perfect system
Unlike the present system, the perfect system (perfect, pluperfect, and future perfect tenses) is extremely regular. The endings for each tense in the active voice will always be the same for each conjugation, with no differences of any kind (e.g, differing thematic vowels; completely different endings, like those of the future indicative; etc.). The perfect active system endings for the indicative and subjunctive moods are as follows:
- Perfect active indicative: -ī, -istī, -it, -imus, -istis, -ērunt
- Perfect active subjunctive: -erim, -erīs, -erit, -erīmus, -erītis, -erint
- Pluperfect active indicative: -eram, -erās, -erat, -erāmus, -erātis, -erant
- Pluperfect active subjunctive: -issem, -issēs, -isset, -issēmus, -issētis, -issent
- Future perfect active indicative: -erō, -eris, -erit, -erimus, -eritis, -erint
Like the perfect system in the active voice, the perfect system in the passive voice is equally regular. However, instead of using the perfect stem and specific endings, the perfect passive participle of the verb and the conjugation of sum, esse, fuī, futūrus in a present system tense corresponding to a perfect system tense (i.e, present ↔ perfect, imperfect ↔ pluperfect, future ↔ future perfect) are used instead, like so:
- Perfect passive indicative: perfect passive participle + present active indicative of sum
- Perfect passive subjunctive: perfect passive participle + present active subjunctive of sum
- Pluperfect passive indicative: perfect passive participle + imperfect active indicative of sum
- Pluperfect passive subjunctive: perfect passive participle + imperfect active subjunctive of sum
- Future perfect passive indicative: perfect passive participle + future active indicative of sum.