Curiously, rejecting the spell design system leaves me feeling free and desirous of creation! So here are some cleric spells, in the idiom of "half-solving level-appropriate problems". As a secondary objective, I want to write some cleric spells that serve as wilderness-level bookends, like Fireball and Fighter's +1 morale.
Duration: 1 turn per level
The subject gains a +4 bonus to rolls to avoid drowning for the duration of the spell.
Spell to compare: Resist Cold. Both situational, don't really address hazards that come up much at low levels, require casting before you fall off the boat. Because they're low-level, though, you can provide protection to multiple party members in the mid-levels when blizzards and capsizing ships become serious hazards.
Cast only in the evening, while in a location where you can see the sky. An omen of good weather appears; when tomorrow's weather is rolled, you may request a reroll of either wind direction or wind strength at sea, or the weather die if on land. The rerolled result stands. Casting this spell multiple times allows rerolling both wind strength and direction at sea, or rerolling a rerolled result.
Spell to compare: Fellowship. Fellowship addresses a common problem at the level of play where it becomes available ("Monster, please don't eat us" vs "we need to sail a long way to hit this wilderness lair") but it does so unreliably (still subject to reaction roll, weather roll) and with a chance to make things worse (can penalize reaction roll, random result stands even if it's worse than the original). Both also require casting in advance of the situation where they're useful, though they're slightly different here - Fellowship gambles resources you might need later, Red Sky expends resources you didn't use today (and thereby rewards cautious play).
Area: 100' radius, centered on caster, moves with caster
Duration: 16 hours
This spell is a great boon to travel by ship. The cleric can alter the direction and strength of the wind within the affected area. They can shift the direction of the wind and its strength by two degrees; altering its direction by a minor compass direction (ie, N to NW) is one degree, and altering the wind's strength by one category (ie, Becalmed to Light Breeze) is another degree. (So if you had a light breeze from the north, you could turn it into a light breeze from east or west, or a moderate breeze from northeast or northwest, or average winds from the north). Once the spell is cast, altering a single degree requires a declared full round of concentration, like casting a spell. Continuing the previous example, if you'd altered the wind from a north light breeze to an east light breeze, and you then came under attack by a sea-dragon and decided that thrust was more important than vector, you'd need to take a round to shift the wind to northeast, then another to north, and then two more to boost it to average winds. Should the caster perish while the spell is active, the winds remain "stuck" at whatever they were set to when he died, until the duration expires or Dispel Magic is cast.
Spell to compare: Create Water. Both make a particular element of a whole day of wilderness travel much easier; while Create Water is limited in the number of people it can support, Fair Winds is limited in how much it can alter a random result. The ability to alter wind direction slowly in combat has a nice "jump drive charging" feel, to draw a Traveller comparison.
Targets: Up to one ship per caster level, all of which must be in the same six-mile hex as the caster. Really big ships might count as multiple.
Duration: 16 hours
The caster can influence winds in a 100' radius area around each target ship, as Fair Winds. When casting, the caster must be able to see all of the target ships (doable from the deck on a clear day, nautical horizon distance being pretty far, but not good in foggy weather). Altering wind direction and strength takes one round per degree of control per ship after the spells is cast. The wind can also whisper messages from the cleric to the crew of each ship - the cleric must name the recipient, and then state the message. There is no provision for replying, however. Should a cleric target a vessel already under the effects of some other cleric's Fair Winds or Following Seas, each cleric rolls a d20 and adds their caster level, with the higher result taking control of winds around that ship, and ties going to the defender.
Spell to compare: Control Weather. Following Seas has a larger area, doesn't require concentration, but is much less versatile, and you still have to work with what the weather-dice gave you. Control Weather gets you perfect control over maybe five large ships (and combat capabilities, via tornado), but at the cost of your wizard having to concentrate and not be disturbed, while Following Seas can give you limited control over many ships.
Are these balanced? I dunno. But it seems to me that if you give the players tools to fight, they will fight. If you give them tools to sail at 6th level, they might decide it's worth a shot.